Howdy! I've played KOTOR on Linux before with mods, and there are two ways I've found that work well for mods:
1. Install them through Wine. Honestly I would recommend playing the whole game through Wine, since it has perfect compatibility, and I've never encountered an issue with it. To make it easier you can use PlayOnLinux (but don't use the built-in KOTOR script). If you wanna try it out and run into any trouble, let me know and I can help!
2. You can install KOTOR and all of its mods in a Windows environment (either an actual machine, or a VM running Windows), then copy the entire game directory in place of your directory on Linux.
Let me know if you need any more help!