I know that they're compatible, but I just want to know if you can apply weapons mods to weapons added by FWE, like the FN FAL. Thanks in advance.

I've successfully applied weapon mods to some FWE weapons, like Desert Eagle and Winchester P94, so the others should be modable as well.

You can add WMK mods to almost all weapons in FWE, there are a few that you can't but it is intended by the FWE team.

Make sure you get the FOIP patch for WMK-FWE http://www.fallout3nexus.com/downloads/file.php?id=4968 - the supported weapons are in the readme

And create a merged patch - required