You should really only use one manager to manage your mods, especially if one of them is MO2. Installing mods with both MO2 and alternative methods leads to MO2 not being in control of all your mods and frequently makes a mess of your game folder-the worst of all worlds.

If you want to add Wrye Bash as a MO2 executable for the purposes of building a bashed patch, there are many quality tutorials about that, including in the pinned topics.

The only thing that you should be including in your bashed patch are the leveled lists. Bashing your leveled lists should have no effect on the Movarth's Lair quest.

I would suggest replaying the quest from an old save (anecdotally, I've never had issues with this quest progressing once Movarth and his goons are dead). A riskier option is to use the console command shown on your UESP page; have a good hard save to fall back on if you decide to try this.

edit: is you actual complaint that the quest is not progressing to the "Report to the Jarl" stage, or simply that your map doesn't show the lair as cleared?

I have no quest from a jarl, just encountered the cave and went in there with followers who were helpful in taking down the master vampire and his group. but yes, I killed everyone and the lair remains uncleared even though I have the unofficial sse patch.

Do you have a save from before you killed Movarth? According to both wikis there are all kinds of things about the lair, buying Windstad, and becoming Thane that can get fouled up if you don't accept Laid to Rest and complete all its steps. Beyond that, I don't have any idea how to set all that right.