There are two techniques, depending on if your scanner has a document feeder supporting duplex scanning.
Check to see if "Input | Mode" has "Duplex Feeder" as an option. This will do two-sided scanning.
If not, then try the following:
1) Scan the front sides of a document to a multi-page PDF file
2) Scan the back sides of a document to the same multi-page PDF file
3) Use the "PDF | Interleave" command
Note that you need exactly the same number of front sides and back sides - there has to be an even number of pages in the multi-page PDF file.