Chris, there's a great deal more to understanding how DMA works! This isn't your daddy's scanner anymore - plug and play it ain't.
Let's start with some basics...(links usually turn out blue...)
http://wiki.radioreference.com/index.php/Main_PageIn this page, you'll find a section called 'Links for Newcomers'. There, I would read the Trunking Basics and bookmark the glossary, which has definitions for just about all the crazy terminology you will run into from time to time. There's also an article there that describes how to hook up your PC via a USB port
Next...
http://wiki.radioreference.com/index.php/Uniden_DMA_FAQI would read- and undestand - the first 4 topics. These will help you to understand what DMA is all about and how to start using it. Pay particular attention to how quick keys are used, and the concepts behind multi site trunking, which your system seems to have...go to the bottom of the FAQ and download the Easier to Read manual
Next...
There is a decent user guide for FreeScan that you can access via 'Help/Online Help'. In particular, pay attention to how FS handles quick keys...
http://wiki.radioreference.com/index.php/Freescan_and_Quick_Key_ProcessingSometimes its easiest to go to the NC forum on RadioReference and ask for a file. FS can import UASD and BuTel software files, but be sure to tell folks exactly where you are (county is good), and that you are using FreeScan to load a 996XT. You might be able to turn up a native .996 file
This takes time to read and understand - there is a Uniden forum on RadioReference as well, where you can get specific questions regarding the 996XT and DMA answered. Patience!
73 (best regards) Mike