Some skills have 10% bonus, most have +10. Also, in the character sheet, the skills have a checkbox for "basic" "trained" and +10%/+20%... skills can either be untrained, trained, +10 or +20. So... is 10%/20% the same as +10/+20? In case they're not, is it rounded up or down?
They are the same.
I've never played (or heard of) Rogue Trader before. But I found a copy of the manual and there are two things to consider. First, it's a 0-100 percentile-based game, so +10 is +10% of the max by definition. Second, look at chapter 3 (Skills), Training and Skill Mastery (page 74 on the version I'm using).
The first time an Explorer acquires a skill, he is said to have that skill trained. Sometimes an Explorer will have the opportunity to acquire the same skill more than once. When an Explorer gains a trained skill for a second time, he gains Skill Mastery in that skill, which grants a +10 bonus to all Skill Tests made with that skill. If the Explorer later acquires that same skill a third time, his Skill Mastery bonus increases to +20. An Explorer cannot acquire the same skill more than three times.
Notice that it says +10 and +20, not +10% and +20%. The character sheet was just typed in a different format. It's quite possible they originally did everything in +X%, then decided that might be confusing and changed it to +X, and the character sheet just retained the old nomenclature.
Further information, the same page says Basic skills can be used untrained, at half the skill's governing characteristic (rounded down). Advanced skills can't be used untrained unless you get a specific trait for it. Once any skill is trained (the first time), you use the full governing characteristic.
So an Astropath Transcendent with 43 Fellowship would start the game with a Deceive skill of floor(43/2) = floor(21.5) = 21. Then at rank 3, he could buy an advance to train Deceive the first time. Now the skill is at 43. At rank 4, he can buy another advance to train Deceive a second time, so the skill is at 53. At rank 5, he can buy his third advance to get Deceive to 63. He could then increase his Fellowship up to four times, with a +5 bonus each time. After the fourth advance, he would have +20 Fellowship, for a total of 63. This would carry through to all of this Fellowship-based skills, so Deceive is up to 43 (base) + 20 (4 Fellowship advances) + 20 (third Deceive bonus) = 83.
It's up to you how to fill in the character sheet, but for the characteristics, I would write as total/half so it would be easy to roll untrained skills at a glance. So Fellowship after four advances would read [(63)31], and you wouldn't have to re-calculate floor(value/2) every time
With skills, I would just check all the basic skills (plus advanced skills you're allowed to use untrained) as "basic" during character creation. Then check off a box each time you train it. Then if you need to roll Logic, you look over and Basic is checked (because table 3-1, page 75 says it's a basic skill). If trained is unchecked, you look at your Intelligence and use the lower number. If trained is checked, use the higher number. If +10% is checked, use the higher number and add 10, if +20% add 20.
This saves you from doing a ton of writing every time you advance a characteristic, but, again, it's your choice. :)