Does Paperport not show a TWAIN option at all? It really should according to Nuance.
If it does, but doesn't find a scanner , have you checkked that it installed a TWAIN scanner when you ran the installer?
Assuming Windows 7, just type into the start menu Scanner and cameras and select it once it shows up.
From there you should be able to add it, or at least configure it properly if it is there already.
As long as it shows up in the TWAIN devices above, they will also show up in Windows Fax and Scan
So at that point you would need to talk to Nuance