I'm having trouble with your mods. There's no instrcutions on how to install them which is quite a problem. I'm a veteran BG2 player and am used to an over-ride folder to extract the downloads into but there's nothing like that in ToEE. Please can someone write up a set of instructions on how to get the smaller patches which have no installer to work.
Regarding the smaller mods, these can be incorporated into the game by placing them in the correct folder (Temple of Elemental Evil/data). This is the override folder for virtually all extracted files from .dat Bear in mind that protos.tab for the main Co8 mod is extensively patched and overwriting it with another protos.tab from a smaller mod will nullify all protos.tab changes made in the main mod. If you could state exactly which smaller mod you are interested in, perhaps the authors of the mod could tell you what the exact changes and this would help to fully incorporate it into a bigger mod.
I was quite interested in the moathouse quest but generally I just pick up mods that interest me at that time and install them. It's just a bit of a change as I'm used to Weidu and extracting to the override folder for BG games.