Almost have enough info to make a character but I've been focused on getting up to speed on the basic combat rules (not spaceship combat or anything). Do I have to use the random roll for characteristics or can I use the suggested point allocation method?
Also, how are we meeting? I'd prefer MapTools for its in-built functionality but I could go pure IRC if it's easier to do that.
When you're attacking something, you roll 1d100. If the result is lower than the skill you're using (Ballistics Skill for guns, Weapons Skill for melee) you hit. Then, to determine hit location, you switch the two number results around (23 becomes 32, etc.) and then you look at the hit location chart. Usually, you'll hit in the body, statistically speaking. Then you roll for damage, which is stated on the weapon. Melee weapons are an exception, because you add your Strength Bonus (The tens column on it: St 40 means your SB is 4, 30 means 3, 57 means 5, etc.) to the damage, and not just what it says.
If you are the one getting hit, after your opponent rolls damage you subtract your Armor Points, and then your Toughness Bonus (Same procedure with the Strength Bonus).
So if you're planning on playing an Ork, you'll want to use melee weapons, as your Ballistics Skill is dreadful. See Cthulhu's for example.
Now I havent played any rogue trader games before but how does having members of the Ecclesiarchy work when Xeno's are onboard?
It probably ends very badly. By all means, do it.