CEP only works with modules that use it. It doesn't affect the Bioware campaign at all.
I understand the same is true of Project Q (but others may know more).
There are no compatibility issues with installing new module files in the appropriate folders - modules, hak, ambient, localvault, movies, music, portrait, tlk - because each module only uses those files specified by the author.
Replacing an existing file with a different file of the same name might break something. However, the only examples I'm aware of are CEP 1 and CEP2 (use only those versions, taking care not to overwrite them with older ones from the Vault, even if the module says you should).
Using overrides and patches is different. In that case, you are changing content in a manner that the module author did not anticipate. So, there is always a risk of incompatibility. This is not a popular message - package fans often want to howl it down - but that doesn't alter the fact. Having said that, the risk may be very small, especially with mods that only change the appearance of the game.
The risk is higher with scripting and gameplay systems. There are known issues with PRC, Tony K and camera mods, for example. They will work with some modules but not others. One approach is to suck it and see. Then if you have a problem with a module, check whether it still happens when the patch or override is removed before complaining to the module author.
