I just wondered whether you knew that using this launcher (probably others do it too but this one works the best for me)
http://forums.bistudio.com/showthread.php?t=89731 allows you to very easily have different mod configs and also run Combined Ops outside of Steam? IE run Steam version of Arma2CO without having Steam running.
Also very easily allows you to have your mods in a different drive/partition/folder etc if you want?
Seems much easier than a CMD file or multiple shortcuts from an desktop organisation point of view to me. You just have a single app to run and can switch between SimHQ, vanilla or whatever with a couple of mouse clicks as well as tie external apps into it like TIR,FRAPS etc so they run automatically when you start Combined Ops.
Anyway might be useful to you or someone else having trouble with the manual methods.
Cheers,
Stonehouse
example pics:




