And you wouldn't be the first one to comment that the manual isn't all that clear - but have faith, there are some alternatives. Put this wiki article in your bookmarks...
http://wiki.radioreference.com/index.php/Category:DMA_Radios_Hints_and_Kinks
First, go for the DMA FAQ. It will take you from the start and get you going in the right direction. Read UPMan's article; use a spreadsheet or other columnar table to help you to set up things the way you want them. There's also a link there that will lead you to an article that has lots about Trunking basics; if you don't understand trunking, before you even think of proceeding, it's wise to understand this first. (Anything in blue is a link...)
While most will tell you that programming by hand teaches you quickly for some it's overwhelming. On the bottom of that wiki article are the 'easier to read' manual links. The BCT15 and BR330/396 links will likely be the ones you will want - the BCT15 is the analog-only little brother to the 996, while the 396 is the handheld brother (although the 396 doesn't have certain capabilities that the BCT15 and 996 do - but you'll find out about that as you read...)
As for software, while most start with the UASD, many want something better. Again, the wiki article has a link for the most popular software for the 996. There are others, such as Trunkstar Elite, that work with the 996 and connect to the database, but to be honest I've heard very little good or bad about this software. ARC996 is the obvious champ, but don't ignore the freeware Freescan package - right now it's programming only (no pc control or logging), but the author is working on that.
ARC996 (and Trunkstar) have the advantage over the UASD in that they both can connect to the database, and you can download data directly, (with a paid subscription). FreeScan and Scan Control can use a copy/paste function to get data into the software. These are real advantages in getting a scanner set up for the first time.
However, just to get you started, jump over to whatever state you are interested in, tell folks that you have the UASD for the 996 (a very important bit of information) and ask if someone has a file you can use. I *think* FreeScan can import UASD files directly - I know Scan Control can (not all software can use the UASD files as an import source).
In short take your time and read. Lay out your needs, and ask if someone has a data file for your area in the state forums. It's sometimes a good idea to get a file you can clone and fool around with, adjusting it to fit your needs. You can add more later.
73s Mike
