Periodically (such as when an item is equipped) compare the base rank of every skill plus the attribute modifier to the actual rank.
For example, someone might have 19 ranks in concentration + 6 from constitution (say, 2 base constitution and another 4 from constitution items) for 25 total -- if they have a total of 43 then the difference is 18, so don't need to do anything. If they had 52 total then the difference is 27 so you need to apply a decrease of 7 to the skill.
You'll also need to handle feats that give bonuses (including (Epic) Skill Foci and things like Silver Palm).
Some big things to watch out for are death (removes such penalties) and Restoration spells -- need to stop them from removing the penalty or reapply the penalty after the spell is cast or the player comes back to life.