Are you having problems with the layouts or how your printer works when it comes to the "refeed"?
In terms of FileMaker Layout design, you just need two layouts based on the same table occurrence (The same exact name must be selected in Layout Setup|Show Records From), one for side A and One for Side B.
You find your records. Add your comments. Print Side A. Change to layout for Side B. Refeed and Reprint.
But how you feed that stock back into the printer will vary with how your printer is designed to operate. Not only whether you have to feed the stock one or a few sheets at a time or all in one stack, but in terms of whether you feed the top or bottom edge of the stock first into the printer will be different for different printers.