What kind of USB Soundcards are you using?
I would approach it by recording with multi-track. Have a multi-input sound interface routed to separate channels and record away. How many scanners are we talking about here?
We need some more detail in order to answer specifically.
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Gear: Digidesign 003R / Telos Zephyr XStream ISDN codec / JK Audio Broadcast Host digital phone hybrid
PC: HP 6005 Pro MT PC running Windows 7 Pro 64-bit w 3 GHz AMD Phenom II x3 B7, 4GB RAM
DAWs: Sound Forge 10 Pro, Vegas Pro 9, Adobe Audition 3.0, Pro Tools LE 8.04, Reaper x64.