TESVEdit Merged Patch is not something you can just click on and make it happen. It takes understanding of each mod and how they are structured and how the leveled lists are formed to make one. So you have to really know the guts of a mod to make it work the best. And, this requires a bunch of manual tweaking.
Bash on the other hand uses Tags that the mod author supplies to help with making the patch. Since the author knows the most about their mod, this makes the Bashed Patch more useful and easy to configure.
However, it is still not a one click thing. When you are in the window for the patch, you have to select each category on the left, see if there is anything in the right pane to add to the patch. If there is, you probably want it included. But, not always, sometimes things show up in there from an option on a mod that you don't have, or sometimes the mod mix your using won't like something being added. If you just think about what is being suggested and your mod mix, it is pretty easy to figure out what should be added to the Bashed Patch and what should be left off.
Nice thing is, if you mess up the patch, the game wont' even launch, so you know right away that it needs to be tweaked. So, add the obvious things, see if the game launches, if so, then exit out, add in the things one at a time your not sure should be there, and see if the game launches.
Not all mods need to be part of the patch. If they do not affect a leveled list or the same cell/object/NPC as another mod, then it can stand alone. But, the tags will tell you if a mod needs to be part of the patch, so don't worry about that for the patch process.
You just have to worry about what mods you load after the Bashed Patch. The mods that don't need to Merged/Bashed together can load after the patch (or before really, most people do that). You can also load a up a mod to test after the Bashed Patch, if you like it, then include it in the patch after.
Always sort your load order before making a Patch if you changed your mod mix.