I am modifying a mod that has a BSA to my personal taste, however, when the cells load in the CK there are only exclamation points on all the new meshes and textures. The BSA is the same name as the .esp and it all works fine in game. Why won't the CK read the BSA?

I should add that I have the newest patch of the CK and the mod I want to adjust for my personal use is the outstanding Dark Tower by Reaper911

you can unpack the bsa and place the loose folders in your skyrim/data directory

You have to unpack the bsa. I think this happens to everyone. I remember I unpacked the bsa when editing the Dark Tower mod too, and after that everything was normal in the CK.

deleted post about a BIG issue

Edit: this is important enough that it needs it's own thread, I will move to another thread;

Loose files always take precedence over those in BSAs, so you would need to extract the HD textures over the normal ones for them to show in game if you've extracted the Textures BSA. Extracting everything won't negatively impact performance, but it might improve it slightly. The potential problem is fragmentation which can be alleviated by putting the game on an ExFAT partition and SymLinking from Steam. Then again, Win7 isn't so bad w/ fragmentation, so NTFS ought to work fine, just never defrag if it's an SSD.