I'm helping my mom migrate from Quicken to CheckBook Pro and she also was wondering how to have two accounts open at once. She uses that all the time in Quicken!
In CheckBook parlance it looks like we want to have multiple entry screens open (one each for different accounts).
Being able to have multiple account registers open at once makes side by side comparisons of payments and transfers A LOT easier than having to shuffle back and forth constantly between accounts in one entry window only.
It was also requested in this thread too:
viewtopic.php?f=3&t=6723&p=12575#p12575