As a new GM with a ridiculous amount of 40K fluff knowledge I have handled setting up most of the aspects of the campaign with the the books and my own knowledge. However I have encountered a problem when it comes to role playing the non combat parts of the adventure in more mechanical terms. My questions are:

1.) How much time do you guys spend between combat, setting up the scene,solving puzzles/challenges, and player questions.

2.) How often do you have to nudge player in the right direction when they are stumped by a problem and how do you go about doing that? Do you have to nudge players even in open ended scenarios?

3.) Any ideas for challenging or common place puzzles for me to use with the group?

Any and all responses welcome, although I do prefer direct statements opposed to sarcasm

I need a little more information on your group if you want specific suggestions, but I can run you through how I usually run things with my group. When setting things up I try and make sure to have an open discussion with my players about the high-level view for my plots, and ask them for feedback so I can adapt my plans to what they want.

1) As opposed to Dark Heresy, our group will sometimes go entire sessions without combat. I present to them a couple of ways to make money or enhance their prestige, and then let them go through with their plans and see how it works out. Puzzles sometimes get problematic, but I do like to usually allow them a diplomatic or swashbuckling route that can allow them to "win" without combat. Other times, fighting is inevitable, but given that they command a dynasty of tens of thousands of crew members, ships that can destroy planets from orbit then powerful enemies will only attack them from a position of strength.

2) Not much. I usually plan out an "optimum" way to solve a scenario, but I let them come up with their own plans and let them roll Logic or Lores to get some information to help them. Then based on their plans, they have to get a number of successes with a bonus or penalty for how much they impressed me with their plan. If their plans fail (and they have), then they have to try something else, or their enemies get a bonus in later encounters. If they're absolutely stumped then an NPC crewmember can be "inspired" to give them a good solution, but again this usually means the subsequent challenges will be harder, or the rewards might be lessened.

3) Have players have to resolve a conflict where both sides are misinformed about the cause of the issue, but believe the other to be at fault. An example would be a rebellion on a Forge World where the Mechanicus calls for aid because their "organics" have rebelled. The Magos started venting toxic chemicals through the facilities to kill all the unaugmented menial workers in response to a rebellion, whereas the workers say the Mechanicus have been dabbling in tech-heresy and have finally snapped and turned on people without issue. The actual cause of the rebellion were Yu'Vath Crystalwisps that had been attacking the Cogitators, but were trapped by the venting of chemicals through the facility. Once the Explorers pick a side or try to resolve the issue, they are loosed and the Explorers will have to try and stop them from destroying the rest of the facility. Based on their action, they may have completely wiped out one (or both) sides, and now have to try and deal with this new threat.

1. I often go 2 or 3 sessions between fights, sometimes more. I prefer RP to blood'n'bullets types of campaigns. Sure, some of the endeavors will simply include more combat, so you may have multiple fights in 1 session. For the most part, I like to keep things RP oriented, but include some fights when they are appropriate. I also allow the players the option of seeking out the fights. In my current campaign, the young RT has inherited a rival along with his Warrant - an antagonist RT that had beef with the RT's father. The players have been seeking out conflict with him since session 1 - and it looking like they're finally going to get their first chance to dance with him 4 sessions later.

2. I try not to give the players answers or nudge them at all. Sometimes, it's necessary when there is a clear and singular way to solve a problem. If so, I give them information that "shouldn't" be obtainable from their investigation rolls (i.e. Common Lore - Imperial Navy offering info on an ancient ship class that hasn't been used in 7000+ years). That said, I try not to craft problems with only 1 solution if I can avoid it.

3. Puzzles can take a lot of different forms - from bookish research in order to find information to a series of complex interconnected actions to complete a larger task. The "what" is up to you - just use your imagination. Just remember that the how is up to the players, always.

1.) How much time do you guys spend between combat, setting up the scene,solving puzzles/challenges, and player questions.

2.) How often do you have to nudge player in the right direction when they are stumped by a problem and how do you go about doing that? Do you have to nudge players even in open ended scenarios?

3.) Any ideas for challenging or common place puzzles for me to use with the group?

Combat seems a small part of Rogue Trader. It's the roadblocks to the challenges, and of course the climax, but that's about it.

I don't nudge players. The group is smart. If they don't get something it's because I didn't get it right or I left something out, in which case I need to introduce something else. Sometimes it's another NPC, sometimes it's just a discovery, maybe some scrap of paper in the Dynasty library, or the remnant of an astropathic message barely received.

The puzzles are the easy part. It's the plot twists that become challenging. Never be satisfied with your puzzles. Once you've satisfied yourself that the puzzle is complete, think of some crazy conspiracy theory and add another layer to your puzzle. That way, when your players have solved the problem, they still probably won't know who was behind it all, and that leaves them guessing.

Combat happens about every other session. Some combats are more cinematic with Command and Tactica skill rolls showing how well they deployed their forces. Some combats are brutal affairs against Chaos Dreadnaughts and Thousand Son Sorcerers while their elite troops try and hold back the rest of the boarding parties.

Pretty rarely, but it happens. Usually my player will just pick an option (often enough, one I didn't plan on) and go with it. I use Logic tests and Lores when they are stuck. Logic to figure out a (usually less than optimal) solution. Lore to remember a relavant fact or story that gives them a direction. NPC Senchenal can be a great tool, as they are masters of lores and can pipe up when you have to nudge them.

When my players decide on a new direction for their endeavors, I think through the parties involved and how they will respond. For example, when my players decided to explore/loot Aubray's Anvil I worked up backstory on how the world worked and how it fell. In my game it was an ancient forge world owned by the KievSteiner Corporation. The world built ships and heavy industrial equipment, including Titan like giant robots for construction and gladitorial battles. When the Men of Iron revolted they were lucky enough to catch wind before it went completely south. Their mildly militant culture and gladitorial titans gave them enough edge to win. Unfotunately, their old enemies the Yu'vath invaded only a few months after they beat back the Men of Iron and wiped them out. The planet is surrounded by debris from those battles. Mixed amond the Archeotech is Yu'vath Void Wasps and smaller Yu'vath constructs. Much of the information is lost due to Crystalwisp infestations. What is designs they have found are often not STC, as the world was too advanced to still rely solely on their STC plans. This will be iteresting when they show some of it to the Ad Mech...