I've made several barcode-enabled programs.
Yes, it is possible to dedicate one scanner for the left side reference and the other for the right side. For this purpose, I recommend using serial interface scanners so the program knows from which port the data comes. ( a scanner with the serial emulation over USB feature also works ). With a keyboard-wedge scanner, the program can just read what comes from the keaboard without being able to differenciate the origin (as it is hard-coded in windows that you can have only one keyboard and one mouse, if you have several, the inputs are merged). It might be possible to set a different prefix in both readers, but low-end scanner don't offer many usefull choices.
I will make a Delphi program to read the scanners and display the result, and a local MsAccess database to record the log.