Setting up mods, addon managers and 3rd party Arma 2 content with OA on steam

[Hovis 0]

So here's my situation:

I have Arma 2 from a disk install bought way back when. It sits on my hard drive, loads of mods, loads of different shortcuts to launch them (as in I don't run them all all the time), ACE updated on it via AddonSync and basically all the trappings of a much loved and abused Arma install.

Operation Arrowhead comes out and I figure I'd move the whole operation to Steam, so I've bought the Combined pack thing, with OA and Arma 2. Fresh start and all that.

I've tried the batch file mentioned above to run Arma 2 and Arrowhead together and it works. But what I'm not sure about is how to run additional mods to Arrowhead or Arma 2 through that. Also do I need both Arma 2 and Arrowhead installed independently on Steam? Also do I place modfolders in Arrowheads folder or Arma 2 on Steam?

Past that, is it safe to presume that things like AddonSync and SIX Updater will work in exactly the same way with a Steam install as they do with a normal one?

So many questions, so few cookies, but those I have go to those who can help. Cheers.