Modding on linux is a little finicky. For all Beamdog's edition, I wrote a script[1] that would symlink datafiles as a lowercase version everywhere (unless they were already lowercase). After this, all WeidU mods were working okay (at least for BG I&II). I have P:TEE but never modded it however, but the process should be relatively similar.

[1]: http://pastebin.com/raw/nmkSGj0L