Not sure if you are still having issues with this, but as another poster said, mods that get incorporated into the Bashed Patch (which is a good thing), when activated, won't have a check but a plus sign so you will know they are merged into the Patch. When you run BOSS, the Bashed Patch is deactivated and along with it any mods that were merged into it. You don't have to re-check each mod that was unchecked; just rebuild your Bashed Patch and when it is done you will see that the mods that had been deactivated have a plus sign, which means they are again activated via the Bashed Patch. I absolutely recommend using a Bashed Patch; it resolves many conflicts and helps to avoid many potential conflicts and much more. Wrye is (imo) the best utility of its kind. Aside from the beginning and advanced help files that download with Wrye Bash, here is a link to a tutorial with pictures (.pdf) by Alt3rn1ty that you might find useful: https://www.nexusmods.com/oblivion/mods/35230