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.
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From there you should be able to add it, or at least configure it properly if it is there already.
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As long as it shows up in the TWAIN devices above, they will also show up in Windows Fax and Scan
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So at that point you would need to talk to Nuance