Originally posted by avatar.zero:

Not automatic by connection from the manager, but it's simple with r2mm on your client machine to just change the profile before launching the game and have it automatically change the mod files for it. In your case it would be even easier as it has "Launch Modded" and "Launch Vanilla" as independant controls, right next to each other on the same screen.

Yup I got it installed on my client and that was exactly what the dr ordered. Seems to be working a treat now. I didnt realize so many of the mods were client side only too.