After a dozen times of doing this, I finally decided to wise up and create a method that would allow for easier tear down and re-build of my load order...
Using this naming method allows you to keep track of the order in which you load your mods. As we all know, the way you load your mods can effect many different things, such as which textures will show up in game etc...
It's simple...
Start naming all of your OMODS like so...
000 - Name Of Mod
001 - Name Of Mod
002 - Name Of Mod
If you find that you meant to put "x" mod where 001 - mod is, you can always do this rather than start renaming from scratch...
000 - Name Of Mod
001 - Name Of Mod
001a - Name Of Mod
002 - Name Of Mod
Using this naming scheme will also allow you to run an semi-automated mod re-install by choosing the "Activate Filtered" option. OBMM will automatically activate all mods according to the numeric order. All you have to do from there is is choose the options for your scripted OMODS.
From there, just import a backup of your Load Order and re-create your bashed patch Use BOSS if you want to double check that your load order is correct.
What are some methods you guys use?
EDIT - Spelling