Every time I make a map w/ a mod it works great during the game. But once I exit and open CC again, i get a 'RTE Aborted! (x_x)' I think because i just extract mods in the main folder, I'm not sure. Is there a proper way to install mods so i can use them in my maps(preset bunker)?

Are you asking how to install mods or how to use mod contents in scenes?
Installing mods is easy. Extract the .rte to the root directory of Cortex, so C:/Cortex Command or wherever you installed it.
Using mods in scenes is a little bit harder. In the mod's index.ini, copy all the includefile lines and comment them out by putting // in front of them. Paste them into scenes.ini under base.rte, before everything else.

Thanks Duh! Well I was asking if I was installing the mods right, because I wasn't able use them in my scenes. Sorry for the confusion.

Never mind.... I get this error for example:

Abortion in file .\System\Reader.ccp, line 530, because:

Referring to an instance ('D80 Yatagarasu') to copy from that hasn't been defiend! in Base.rte/Scene/Floating Isles.ini at line 10!

The last frame has been dumped to 'abortscreen.bmp'

What else should I do? Now my scenes wont save at all at given maps like Grasslands and Horiz. Please help, also note that I don't know Lua.

*Sigh*

Look. You added a DarkStorm dropship to your map. Base.rte loads before DarkStorm.rte (or whatever).
So the DS is not defined. The game needs to load the dropship before it can place it to the scene.

My suggestion, don't place your custom scenes to Base.rte.

Thanks, got it to work.