Just thought I would quickly pop in here officially before I respond in length to Kelmych.
It has been a while since I have worked on my own patches, what with work and my programming course, but the issue I had was that in some cases a bashed patch would incorrectly carry over records or merge records from other mods that I SPECIFICALLY chose to leave out BY HAND in order to carry over balance aspects such as in the case of FWE.
So it is not as much bashed patches don't work as it is a specific request I have to ensure everything works as intended. ::
I wouldn't put up such a warning if it were not absolutely necessary. You can bash and merge as you wish with every other mod out there (subject to any author notes etc.) but my patches should be loaded as stand-alone overwriting patches as the changes are required. You can however (and I ABSOLUTELY recommend it) merge all the patches safely, once you have them in the correct order as specified (in the case of multi-patch patches). The latter is an unfortunate side-effect which I hope to correct in due time with an even more streamlined installer.
Sorry for any confusion caused, I hope I can clear that up as well.
Deadmano's post in FO3 doubts about Wrye Flash was marked as the answer