To be honest I don't know that you can. If you just set up a test instance and open Excel twice, because that is what you are talking about happening, if you name one workbook "test1" and another "test2" if you try to move a workbook, or even a worksheet between the two applications they are totally unaware of each other. I also notice odd behavior while simply manually cutting and pasting from Excel instance 1 and Excel instance 2.
You may have to write two macros kind of a drop off and then a pick up from a location that you share between them. Maybe a command button on the tool bar.
Maybe one of the super excel guys on here have a better answer.