You're mixing apples with oranges and coming up with grapefruits. The ARC996 software I presume you got from Scanner Master does not 'go on' your scanner; you must connect your 996 to your scanner so you can program and manipulate data for it, as well as to have it control it.
You will need to decide which jack you want to use for PC control; it should be noted that if you decide to upgrade the firmware in the scanner (think of the 'brains' of the radio), you have to use the front jack. You will also need to say whether you have serial ports on your PC (most new ones don't) or you only have USB ports, which means you will need a USB-serial converter. Uniden sells them (their USB-1).
In the meantime, read (and bookmark) this site - much better than reading the 996's owner manual... (note anything in blue or underlined is a link)
http://marksscanners.com/996/996.html
Since you got ARC996, you can get a premium subscription, and download data directly from this site's database. Here's the procedure...
http://www.radioreference.com/apps/subscription/
Just like any hobby, there's a ton of terminology. This will help - just click on the term and you will go to a little article that defines it...
http://wiki.radioreference.com/index...ry:RR_Glossary
The 996 has many newer features - this will get you introduced to them...
http://wiki.radioreference.com/index.php/Uniden_DMA_FAQ
There is lots of stuff to learn here. Take your time - bookmark these, read them, then come back and ask questions. Questions about the 996 should go to the Uniden forum; if you have questions about your area, they should go to your state's forum.
73 Mike