Right, I believe I've got one last problem before I can really get on with my playthrough. Well, I've just started experimenting with merging my armor and weapons with http://skyrim.nexusmods.com/mods/37981/?tab=1&navtag=%2Fajax%2Fmoddescription%2F%3Fid%3D37981%26preview%3D&pUp=1 mod. I've got TES5Edit routed through MO, so it's a matter of using the merging mod through MO. The test itself went pretty well. Although I didn't manage to do multiple mods all at once, the one mod I did do worked pretty flawlessly. Yep, I tested it and it worked just as well as the original! Now the problem. Once I merged the mod into a new custom plug-in I found it only showed up in the right hand screen on MO, but it doesn't show up in the left hand screen. I checked the MO mods folder and I can't locate it. Anyone know where it could be storing my new plug-in? If not, is there a way to locate my new custom plug-in through MO?

check the overwrite folder (..\Skyrim\Mod Organizer\overwrite) or else just the data folder (..\Skyrim\Data)

If I understand your question - in MO, only installed mods are in the left panel, while in the right panel, there are ESPs and ESMs, which appear/dissappear on mods installation/uninstallation. The newly created ESPs, like Bashed Patch or in your case the merged patch, are not installed, they are single ESPs and are therefore only in the right panel (possibly under Overwrite section?). It is perfectly OK, as you don't need to have the ESP in the left pane, you can just activate/deactivate the patch. On your game start, all activated plugins in the right pane are loaded... I hope I am making myself clear:-)