I've been running Rogue Trader for my old Dark Heresy group for a while now and it's really bedded in. In fact I've been surprised by how well - to the point that I can't concieve of running anything else for the forseeable future.

However the point of the post is this. Through fair means and foul it appears likely that our player's dynasty may soon aquire the use of two more vessels, leading to a burgeoning fleet of three (two transports and a light cruiser). I'm find with that at the moment (toys can always be disabled/lost/stolen etc) but I wondered if anyone had experience of runing players with a "fleet" and how they handled it. Was there any pitfalls to watch for? Did your players split over the ships or have them run by NPCs?

All thoughts & suggestions appreciated.

Don't let the party split up over multiple ships on a regular basis. Quite aside from the extra hassle it'll put on you, it's worth remembering that NPCs are people too! Unless they're acquiring the ships directly from the builders' hands (either as a new-build, or as a recommissioned hull directly from mothballs), there'll be a well-entrenched society and hierarchy with a presumably stable set of power relationships aboard. Putting a new command staff aboard is going to upset those relationships- there'll have been people working their way up the chain of command for potentially decades, and they aren't going to be happy someone- and an outsider at that- has been brought in above them.

For that matter, anyone else brought in, at whatever level is going to be just that- an outsider. Ships' crews tend to form their own society, wholly distinct from that of any other, and there is a distinct trend to the insular. Outsiders will not be appreciated, even if they are part of the same fleet (although those from within a fleet will find less friction with the crew). Admittedly, this will be less and less of a problem the longer the various fleets are integrated, particularly if they don't get sent off in radically different directions for Background Endeavours, but it's not really going to go away.

So, work up NPCs of the other ships' Captains, First Officers, Astropaths, Vox Officers and possibly Navigators at the least (those being the people your party are most likely to interact with), and if they aren't being sent off on a Background Endeavour (which I can't give advice on, I'm afraid), then use the squadron rules from Battlefleet Koronus.
If your players insist on regularly controlling things on the other ships then either remember to play up the initial resentment (and hopefully eventual acceptance) of the Outsider coming in to run their ship, or turn the relevant NPC into an alt-character. Hopefully, they'll stick with the Dynasty's flagship, but you never know.

Personally, I found that providing the players with more ships actually made things more difficult - and entertaining - for the players. With the PCs spread out across the ships, they couldn't stack their abilities as much, while they could coordinate their actions and execute pincer maneuvers, or have one of the ships sneak behind a blockade in Silent Running while the others attracted the fleet's attention

I would suggest using hte NPC actions rules in BFK for the ships without PCs on them. It'll make the combat go a bit quicker.

On a similar note, how does a GM handle multiple warp capable ships? Does everyone just follow the flagship and forgo the individual navigator rolls or do any of you actually roll to determine when and where the other ships exit the Warp relative to the flagships intended destination?

In general the fleet that sticks together, survives together. I just rule that as long as everything goes fine for the leading vessel, the fleet will make it through intact. However, if you should happen to lose the Astronomicon or have enough serious warp encounters, you may find your fleet comes out somewhat more ragged than before. I try to avoid arbitrarily taking away their ships though. usually I just inflict some morale/population damage.

The benefit of having more ships in your fleet is that they can keep themselves busy with the routinejobs. Things like making sure those trade contracts you've made earlier have some ships plying the route. Of course it is not bad to have some ships working as a small fleet, for example having a transport with you can be very handy. So does having a squadron of destroyers or that ship with the IG units inside.

Things can get a bit out of hand with those fleets though. Can you imagine needing a fleet for quite a few small scale endeavors? There are unfortunately not enough rules for the need to pay up for all those assets. Running a ship costs money, running a fleet should cost fortunes. Bringing a fleet to an endeaver that doesn't need it, is a waste of money. At least it is when I run things.

My group has gathered a total of 5 ships so far, with a sixth (batllecruiser) in drydock around the Lathe's. They have acces to a Dauntless class lightcruiser, a Falchion class frigate, a Cobra class destroyer and two transports. The lightcruiser, the Praetor of Laconia, is their flagship, cruising around the expanse is done with this ship. Both transports are engaged with ferrying their produce to Port Wander and the Lathe's, escorted by the frigate. The destroyer is employed running between the two planets they hold, as a source of early warning and protection. The destroyer sometimes escorts their lightcruiser, whenever they're expecting trouble.

With their ships splitup like this it keeps the hassle for me to a minimum, and gives a usefull source of 'problems' I can spring on them.

A potential pitfall is the change in the dynamics of space battles.

With multiple starships in a fleet:

1) More ships are needed in space combat to keep things interesting. As a result, it becomes more likely smaller ships can get worked over.

2) It becomes more likely that ships will get heavily damaged/disabled in a fight. This, in turn, can lead to the heroes capturing more ships.

Not insurmountable obstacles by any means, just things I've had to deal with.