Pg. 159 Inquisitor's Handbook (IH) for costs of a ride on a ship.
As for Pilot skills test, refer to pg 105 DH Core book and pg 235 IH for more information. Pretty much, it's all narrative. Like say your PC's are raiding a Cultists Hideout on a moon/desolate area or a Space Station. These areas probably have ground-to-air defenses. So, once the shooting starts, your PC tests to see how well he dodges with the ship (ship being gun-cutter size). Or maybe a freak storm hits the ship, a veracious winged predator attacks the ship, someone sabotaged the ship and both engines are blown, etc etc. So, the PC needs to test his Pilot Skill to see how well he can dodge/evade/land/not crash. Maybe passing gets them safely landed, failing gets them 1d5 damage +1 per degree of failure, and passing superbly gets them closer to their destination before the PC has to land.
As for playing NPC's on a RT ship, all you have to do is create names, descriptions, and a few quirks for about 3-6 NPC's on the ship. These would be (when referring to page 224 ItS "Ship Roles")
1) First Officer (or whoever the PC's delegate to be in charge of the ship while they are all planetside)
2) Engineer Prime (Tech priest in charge of all the other Tech-Priests, so, Scotty)
3) High Factotum (A Seneschel type character / Spy / Diplomat)
4) Master-at-Arms (person in charge of Security)
5) Choir Master (Astropath)
6) Warp Guide (Navigator)
Obviously some of these roles could be played by a PC, so you can skip them as needed. Your stats for these characters can be from other NPC's already in the books, unless you want to create a whole character sheet for them ( I had a palyer who loved creating characters, so I allowed him to and he want all out on these NPC's). Referrencing RT pg 370-375 the First Officer can be a Free Trader Captain, Navy Officer or a Void Pirate Captain (this all depends on your PC's); Engineer can be a Tech Adept found in DH pg 336-345; High Factotum could be a Dissolute Noble or a Merchant Magnate from DH; Master-at-Arms can be a Navy Officer or Oathsworn Bodyguard from RT or an Arbitrator and such from DH; Choir Master an Astropath from DH; and the Navigator….. yea…. that one you have to flesh out a little more if you want stats. Mind you, some of these classes, like the Astropath, are lacking in a few things, so buffing up a few stats by +5 or +10 and giving them a few additional talents, traits, powers (like Astropath getting Astral Telepathy, etc) and/or equipment is a good way to make them fit in better. All I ever did was take one piece of paper, write down who it was with a description and any quirks they had, their stats below this with equipment, powers, talents, skills, and traits. I could fit everyone of importance on that one piece of paper, with extra space for when the PC's made someone else important and all I had to do was jot down a name, brief description and and their occupation, with no stats or anything else. Like a Pilot they liked having fly them around, or a Priest they preferred confessing to, etc etc.
All other NPC's of importance I kept on a separate piece of paper. Like the Governor they left in charge on a colony they created, or a Free Trader Ship Captain they saved and wanted to keep contact with, a Navy Officer who's ship they hailed, taunted, and then hid from, a Criminal boss they crossed on Footfall, etc etc. Pretty much just names, description, who they are, and why they are important now.
As for using RT rules for DH, yes and no. For vehicle combat (like Aerial Dog Fights) yes. For other stuff, it depends. I wouldn't do to much crossing over though, because then it would get really confusing. Best of luck to you.