I use WIn500. Thus, my reply is based on my experience with Win500 vs. the PSR500. I am by no means an expert with this, but I did this 6-7 times over the WE getting my new 500 up and running as I like it.
1) Set up the software like you want it ref your desired scanner set-up
2) Save the software settings as a file (File--> SaveAs, Name the file, save it to your PC)
3) Connect the USB cable to your computer. Make sure you have no driver or computer hardware issues relative to the cable.
4) Connect the USB cable to the scanner
5) Turn the scanner on
6) GO to the scanner menu (I think) and select "Upload to Scanner"
The scanner, as well as Win500, will show the upload progress (pretty quick in my experience). Upon completion of the upload, the scanner will reboot itself, and, assuming you did everything on the software side correctly, you're in business.
7) Un-plug the cable from the scanner.
Hope this helps a little.