The only thing that seems strange to me is to bond two nics and them have the connect to two different Switches.

I guess this is possible, but I'm not sure the advantage, especialy if you are using MPIO.
I believe in MPIO you set two different Virtual IP's. If you can, check the video.

http://www.vimeo.com/moogaloop.swf?clip_id=18113062