Ok, Preface first, I managed to run PKHeX on Linux, although I haven't test whether the edited save works or not because I didn't have my game atm.
Anyways this (hopefully) should be foolproof, considering I'm one and I managed to do it.... Oh and another disclaimer, don't expect the GUI will be pretty. Btw, I'll try to be as concisely as possible, I'm on my phone writing this.
1. Install PlayOnLinux. It's hassle free Wine from my limited experience, no need to manually set pref