So the mods I got only appeared in Skirmish mode and none of them appeared in Editor mode. Result is I have to create a map without brains or leave out bunker pieces so that when I actually test it, I can add those manually. Any way to change this? kthx

The mods have to be included in the index.ini in base.rte.

When I add the mods to the index, do I have to delete/move something or is just adding them to Base.rte's index enough?
I am copying and pasting from the mods's indexes to the Base.rte's index. Is that how your supposed to do this?
Sorry to be a bother but I'm still new to CC's stuff

Well look, if you simple copy all the IncludeFile lines from the mods into the base.rtes own index.ini, it will load the mod twice. So either use cut and paste rather than copy, remove the lines from the mods except the DataModule one or comment out the IncludeFile lines with // before each line or /* "stuff here" */.

If still confused, I suggest to look at the BMCP:
viewtopic.php?f=61&t=12026
The integrated version overwrites your index.ini in Base.rte with one that includes all the modules in the pack, so you can use them in the scene editor. If they aren't enough, you can look at how it does it to add any other mods to the scene editor.

Oh, and if you get any errors, read the readme.