There is a set of rules (called LEA) that some people follow, but I have found too many exceptions for the rules to be helpful. For example, some Alclad II lacquers are recommended to be applied over a gloss black enamel.
If you are layering different paints, there are a few rules that will help.
1. Always test on something other than your model. I have a couple of toy-like AFV's that I test different combinations on. When I'm done, I just strip the paint and test something else.
2. Always let the paint fully cure before you apply a different paint on top.
3. Always apply the different paint in light coats. This helps prevent the solvent from dissolving the underlying paint.
These rules are not guaranteed to work (some paints are just not compatible), but as long as you follow rule 1 and always test, you won't ruin any models you care about.
Chris