Apologies if this is common knowledge...
When I find a mod on Steam that I cannot live without (i.e. the very cool Morrowind armor pack that was mentioned a while back) I convert them to a NMM friendly archive file.
Locate the files
Archive them
Pull the archive out of your data folder
Install the archive using NMM
I thought I was an evil genius when I discovered this. I'm sure alot of people are aware of this but if not...cheers.