Let's see what happens by tinkering a bit with an example character.
We have, let's say, a first level warrior.
This warrior has
- 4 ranks in swim, which is a class skill
- 1 rank in climb, which is a class skill
- no ranks in jump, which is a class skill
- 1 rank in use magic device, which is a cross-class skill
- no ranks in tumble, which is a cross-class skill
He gets a +3 bonus in swim and climb, because they are class skills and he has purchased at least one rank in them.
He has no bonus in jump and tumble, because he has no ranks in them.
He has no bonus in UMD and tumble, because they're not class skills.
Now he levels up and takes a rogue level. He puts all his skill points in jump.
Being both rogue class skills, tumble and UMD are now class skills for this character too. He now gets the +3 bonus on UMD, since he has a rank in it.
He also gets the +3 bonus on jump. He would have gotten this even if jump wasn't a class skill for rogues.
The number of ranks you invest is irrelevant, as long as it's at least one.
So if your warrior/rogue puts all his ranks in a cross class skill for both classes, he does not get the +3 bonus.
I think the confusion comes from this sentence of yours:
It tells that class skills are automaticaly added to my skill list with bonus +3
No, it doesn't do that.
Your class skills are not the skills with the +3 bonus.
It's the list of skills that can get a +3 bonus, provided you buy a rank in them.