[quote=EnderDragonFire]
@TJ When I need to mess with mod priority I just launch MO, but that does not happen very often because most of the mods I use have no resources/BSA files with them. Most of what I need to do on a regular basis consists of disabling/enabling and moving around ESP files that I am working with. FOMM is better for that purpose than MO, at least in my opinion. 
[/quote]
I have to see what you are doing to know exactly for sure, but to me it sounds like that would be easier using profiles in MO.  I currently have (4) Profiles - Default (Which I don't use), GECK (currently for Mod conversion and hopefully creation before FO4 ... lol), My Character, and Sandbox (testing mods).  After testing a mod I like in Sandbox from either conversion or download, I can activate it in the Character's profile and deactivate it in GECK or Sanbox.  If I am converting a mod, I can use the GECK profile without effecting my character's profile or sandbox.  I can create another profile just to either play Fallout New Vegas characters or another TTW character.  I can enable and disable mods in any profile or configuration files without effecting the other profiles by either installing/uninstalling it or unchecking the ESM/ESP.  If a mod that installs multiple .ESPs that I know I will not be using in any profiles, like Nevada Skies - Basic, I go to FNV > MO > mods > mod folder and delete the ESP.  If I need it later, I can add it in back later.