Thanks for your post, this is Andrew from BackupAssist support.
The easiest way to achieve this I would suggest you go to the Schedule tab in BackupAssist and choose the 'Custom' rotation scheme and then click on Modify you custom scheme. From here you can choose the type of backup to perform each day (full, incremental,etc.) and you can also specify which days you want each to run.
If the drive letter assigned to your USB drive does not change when you swap it each week, you should have no problems.
I hope this helps, but please let me know if you have any questions.