Which version ? Start with a new project, select your sub and the type of box you're thinking of using. The vega 124s are in there... think the others are as well.
Then you'll want to input volumes, have it figure port length. It's not particularly useful except for helping to show the flat response curve you're looking for with varying conditions (I dare say it might be most useful at telling you how far messed up little errors will be... and putting your mind at rest). I'm not a very power user of the program, but it helps hone in on what size box and port you want to use. BTW, the dimensions it gives for boxes aren't very good... while they may end up with the right volume, they just seem out of whack as far as proportions.
97 VW Jetta - building a system from parts in my old 85 Jetta
HU: Pioneer P740MP with 12 disc changer
Front: 3.5" JBL GTO302s in dash
5.25" Cerwin Vega Vega Series 502s in door
Amped: US Acoustics USX-2050 @ 2 ohm
Rear: Stock components
Sub: Single 12" Vega 124 in a cheap bandpass box
Sub Amp:US Acoustics USX-2150 bridged