When you have cubemaps in a map and you finishing compiling and then building them. Do I use the bsp that is saved in ep2 or were I have it saved?

Yes, they are inside of the BSP in the maps folder.

Hint: For almost all (especially short) questions:

In the maps folder of what? EP2? Or were I have them saved?

And I will be sure to ask there next time.

when you build the cubemaps it saves the cubemap data to what ever BSP file you were running when you compiled them

Alright thanks