I've been waist deep in the RT core book, wanting to make sure I get all the fluff details 'just right'. I was curious though about how RT fleets are organized. Do they usually just have their one warp capable flag ship which jumps system to system maintaining a bunch of non interstellar fleets? Or do they have a bunch of Warp capable vessels that move with the main ship? It seems from the fluff that ships with Warp drives are extremely rare, but other passages suggest otherwise. Any advice would be appreciated, thanks.

Well, it entirely depends on how long the Rogue Trader has been around. A brand new one would have one ship and no fleet of any kind, where as a RT that's been around for centuries would have fairly sizable fortunes and fleets.

I imagine the Rogue Trder and his ships go through phases. He starts off with all the ships he can get going everywhere and doing everything. Then it transpires that after the first few ships, he's spending more in fuel than he's making by having the ship there.

At this point he'll either dock the spare ships somewhere, picking and choosing depending on the mission, or appoint an underling to manage Fleet B which goes off and makes profit on it's own. Either way, fewer ships in one place.

So anything more than five RT ships in a single fleet is horribly impractical. I'm talking big ships here, the guncutters, system-craft and escort ships don't count.

A warp drive is rare, but not forgotten technology (I think). New ones are going to be sent straight to Imperium officials or the Navy, so RTs have to make do with second-hand ones.

There really isn't anything like an average RT. One might be head of a huge dynasty with dozen of ships and several fleets. Another might have a ship or 2 but lead a fleet of allied ships. While others might have a single ship which they can barely afford to keep fueled, and maintained. The PCs by the rules start with a single ship and enough resources keep it maintained. Plus enough to fund their own fairly high end equipment.

The main RT book is vague about the RT's other holdings outside the ship the PCs are on. It's implied that they have sources of considerable cash flow outside of what they are earning from their adventures. This could be factories, estates, investments or even a chartist* merchant vessel. Generally a GM should work with the PCs to define what the source of their funds is.

*Chartist ship are warp capable ships with a charter to trade between several system or within a subsector or sector. They have no navigator so they can't make jumps of more than 4 or 5 light years. Generally they ply a fixed route with a (mostly) fixed cargo.

Its in my understanding and experience that any Emperor fearing Imperial Starship entering the warp needs two things. Warp Drives, and a Gellar field generator. The Warp drive is needed to direct and control the vessel while riding the currents and swells of the Immaterium, while the field keeps a much needed bubble between the living souls of the crew and the stuff of Chaos, keeping them safe from becoming instantly ripped from there bodies and the very hull of the ship from melting into a mockery of what it once was or becoming haunted by demons. A ship going into the warp without a Field will be instantly consumed, and even if it had one, and no drive, it wouldn't even be able to open a portal into the warp in the first place, or be able to do anything to keep it from simply being cast adrift, with no way to leave the Immaterium.

Any ship that enters the warp ether has to have its own Gellar Field, and warp drive, or it needs to be literal attached to a ship or device that has them both, and is able to project its Gellar field out enough to shield the other ship.

And the issue of rarity is kind of misleading. The Imperium of man is a vast and powerful entity, that requires constant trade and distribution of resources between its planets. To fill that need, they have warp capable vessels. Almost all FTL, Warp drive ships are controlled by the Imperial Administration and its agencies in one for or another, and while system ships are easier to construct, with about a rough estimate of at least 5 to one warp capable vessel... the Imperium is ******* massive, having over a million inhabited worlds that are active member that contribute to it resources. So, there are a lot of warp ships, most owned by guilds of traders, with the more powerful warships belonging to the Imperial Navy. All of which have a connection or debt to the Tech priest of Mars that are the most likely ones to have built the ship on commission, and keep it running from the lowly bulk transport preyed on by all, to the mightiest war vessel. A Rogue Trader is one of the few 'legal' ways of having your own Warp drive equipped ship.