The WinISD version that I'm familiar with is the newest alpha Pro version http://www.linearteam.dk/default.aspx?pageid=winisdpro and I am no WinISD pro myself. But if you have an older version you may want to download this one. They also have a message board for questions.
Many of the quality amps that are used for sub bass output have an active subsonic filter, usually variable from 20-50Hz. If your amp has one set it to between 20-30Hz. Subsonic filters can be built, too, but is fairly complicated as you would be building a passive type. I'll list some links for you to study, but you should look for either an amp with subsonic filter or a separate filter if you intend to use a vented enclosure. After the rumble is filtered out, you'll use the LPF on the amp to limit the high freq that the sub gets. So, in effect, the sub is filtered at the low point and crossed-over at the high point. This high point crossover frequency is also the low point crossover freq for the mids and highs in the car.
1. Use the info in your amp manual for what db/octave crossover slopes it uses. Once you know what filters or crossover slopes you will be using, then you can input that into the program. Find more from their help or help forum.
Here are some links for info in general:
http://www.users.bigpond.com/bcolliso/active-filter.htm
http://www.diysubwoofers.org/prt/ported4.htm
http://www.partsexpress.com/resources/crossover/xoverfaqs.html
http://www.users.bigpond.com/bcolliso/active-filter.htm
https://www.the12volt.com/caraudio/cross18db.asp
3. How would the program know the details of your particular car or installation? Remember, this program is also used for in-home woofer cabinets.
Other, please use the version I linked to. As I said in the first post, choose one sub that is preloaded in the database. I looked at the Image Dynamics IDQ12D4V.2 for reference as I wrote this. Choose as a new project. You get a dialogue box in the center of the screen. Click through it from next to next....it chooses an allignment that is as smooth and close to .707 flat response as possible. (Working with a vented project doesn't show allignment value, I think. Working with a sealed box does...who knows?)
But, nevertheless, to compare one allignment to another....leave that graph on display and click "new project" again. Choose the same sub again, and this time when the box displays "Super boom-box", change it to quasi-Butterworth instead. Finish out the dialogue box and a new graph will appear with the first one. You will see the difference in output: one is a smoother rolloff, the other is a sharper bottom end rolloff but with extended low freq range.
As I said, I am no guru with this program and you'll find other help through the 'winisd forum. The links I gave you have a lot of info you can learn. Remember that building a successful vented enclosure usually comes with a standard prerequisite of having first built successful sealed enclosures. It's all about experience and knowledge, so learn as much as you can. Here is one more article you will find useful: http://www.ivhs.k12.il.us/~andrewt/veisd
Build the box so that it performs well in the worst case scenario and, in return, it will reward you at all times.