You can set up a scan when you create a new device in System Preferences:
go to System Preferences --> FCSVR Pref pane --> Devices Pane and then choose create new device ("+" sign and the Device Assistant will appear. You choose the type and then you can set up a Full or Add only Scan here.)
Other option is to set up a Scan via the Administration window in the Java Client:
This is not as easy since there is no Device Assistant.
go to Admin window in Java Client --> Response and then create a new 'Scan' response on the device you want to scan. 'Scan Productions' is something different, maybe you want that instead, I don't know. Depending on how you set it up, it can create a Production in FCSVR catalogue for each folder or subfolder and that media will be scanned and placed into that Production in FCSVR catalogue.
Anyways, once you create the Scan Response, go to Admin pane --> Schedule. Create a new schedule and add the 'Scan' response you just created to the "Response List" section. Don't forget to check "Enabled"...can't tell you how many times I created the response but then forgot to enable it.
Once you scan the assets, they are in the FCSVR catalogue with clip proxies, thumbnails and posterframes. If you have existing FCP projects that use this media, you will want to make sure the media in the FCP project is connected to that same media that was scanned. When you upload the FCP project, it will not dup the assets, just add the FCP project to it, unless you didn't set the EIP device correctly. If you look in Search All Jobs, the only thing that should be generated at this point it Edit Proxies (if you enabled them) and Elements.
Now my question to you is the same as Chris' question here
http://discussions.apple.com/thread.jspa?messageID=9147105#9147105. How did you set things up so far? What is your workflow? Where is your media?