Here are the total rules for skills (in my own words):
Each level you get a number of skill points based on the class you choose to level up as.
You may spend these points on class skills for the class you are levelling up, in which case one skill point gains you one rank.
You may spend these on skills that are not class skills for the class you are levelling up, provided they are not exclusive to another class. In this case one skill point gains you half a rank.
You cannot spend points on an exclusive skill unless it is also a class skill for the class you are levelling up.
The maximum ranks you may have in a skill are determined as follows:
If at least one class the character has taken has the skill as a class skill and it is not an exclusive skill, the maximum is equal to your *character level* + 3.
If none of your classes has the skill as a class skill and it is not an exclusive skill, the maximum is equal to your *character level*/2 + 1.5.
If the skill is exclusive to one or more classes, if you have one or more of those classes, the maximum is equal to the sum of those *class levels* + 3.
You may spend any number of points on a skill when you level up, as long as this does not raise it above the maximum ranks as determined above.
It's a little bit complicated, but if you go through the steps one by one you'll see it makes sense.
-The Souljourner