Hi there acs14007,
Yeah, it turned out really simple. I just put everything in a single schematic and created two board outlines in the pcb layout tool. Double-click to define one, drag it elsewhere, then double click again to define another rectangle.
This technique has some issues though:
1) the flood fills don't work properly when there are multiple board outlines. I have brought this issue up to Upverter support, but I am sure they'd appreciate another reminder . As a workaround you can layout your components on both boards, then delete one of the boards, do your fills, then recreate the one you deleted and delete the other outline, do the other board fills, and finally recreate the other board outline.
2) in order to avoid drc failures, I named the signals and planes differently on the second board, even though they would eventually connected (VCC and VCC_2 for example)
I ended up using this strategy and it the boards produced via osh park actually came out great.
I will post a link once I am ready to share my design.