I've been running a Rogue Trader campaign for a good while now, and I feel your pain. I think
FFG are good at setting and production value, but their rules are over complicated and often buried in paragraphs of text. The books layout doesn't help, as you must often flick between several different areas to get what you need.
Some stuff that might help:
- Read up on how
RPGs in general work.
- Get the
GM screen, it has summary tables on it.
- Download and print several copies of the
RT Quick Reference document the lads on this website have done.
http://darkreign40k.com/drjoomla/index.php/component/docman/cat_view/36-handouts
Another point: Generally, you're better off starting the group off with a smallish ship. Give them something too large and you might find it difficult to challenge them at first.
Lastly, talk through character creation with the group and decide why they are working together, and most importantly, who is going to be the Rogue Trader. It's really important that the player playing the Trader understands that the game is co-operative and fun for everyone- I was pretty lucky in that my Trader was a fairly hands off manager, which let the various underlings shine.