Heh, it's never too late !
MOUL, Gehn, etc, shouldn't be affected by installing DI - the only conflict might be with Complete Chronicles.
If you played Complete Chronicles without installing the Offline-KI or new content with Drizzle, you can install DI on it (but you won't be able to play offline anymore). Otherwise, it's recommended to uninstall and delete the remaining files, then reinstall a clean Complete Chronicles to avoid issues.
If you want to keep BOTH an offline version of Complete Chronicles AND a version of DI, you can copy the whole Complete Chronicles folder (where UruExplorer.exe is located) to a new folder, and install DI in this folder.
Then you can use Drizzle to install the Offline-KI and new stuff in Complete Chronicles' folder. You don't need to use Drizzle to modify the Deep Island installation (except for MOUL/Myst V Ages).
Multiple versions of Uru can run in different folders (no matter their version), but Complete Chronicles' installer usually doesn't allow you to create two distinct installation folders for the game - that's why you need to copy the files yourself to a new folder where DI will be located.
Hope that was clear enough !