Justin,
Yep, that makes a big difference. Once you have done your development and testing on your desktop and you are happy then in FlashBuilder you choose from the "project" menu "Export release build" and then you copy the contents of the bin-release folder over to a virtual directory on the server. Quick IIS tutorial: open IIS on the server expand the websites node and right click Default Web Site and choose new Virtual Directory. Click next in the dialog and give it an alias like FlexViewer and click next and browse to the folder that you copied the bin-release folders contents to. Click next and then ensure that Read and Run scripts (such as ASP) are both checked. Click next and then Finish. That's it your ready to run from the server.