Well, I come from a different perspective...as a developer, I like to keep seperate dev and test environements. To do that with Skyrim, I keep two folders on my machine:
\SteamApps\common\Skyrim.DEV
\SteamApps\common\Skyrim.TEST
I drop the extensionn to use that environment (folder). So while I am deving, Skyrim.DEV is just Skyrim. When I'm ready to test, I rename the folders. It's very quick and easy and keeps everything completely seperate. (I actually maintain a clean image of each skyrim version on my network drive so I can always revert back if/when needed. This has proven VERY useful to test new Skyrim Beta Releases and when updates screw everything up. I highly recommend this approach if you have the drive space.)
Having the complete Skyrim folder seperate was the only way I could "test" the 1.6 beta, but still "dev" on 1.5. Just had to rename the folder.
When I'm ready to test my mod, I build the BSA file. I keep all my mod install images in their own folder, so I make the BSA from that install image. (I always make my own BSA images, I never rely on the CK to do it properly, as it didn't.)
I hope I make sense. The rename process takes just seconds and I always know which environment I'm working with by looking at the other directory names.