if you add --load-balance in miner options it makes some judgement of which pool to use based on efficiency, but I've heard it has some problems.
I should add the preference to set different config files for each window rather than one for each which should let you do what you want to.
Thanks for the reports, I'm hoping to make the 1.4 branch the old stable version to the forthcoming 1.5 branch!
Thanks for the info. I'll play around with it.
Another cool option would be the ability to add new instances of the mining engines (with a new window and config file for each). That would obviate the remaining advantages of the command line miners for OS X. It's super easy for me to suggest that, but I bet it wouldn't be all that super easy to do.

You could call that MacMiner Pro and charge directly for it.