Damping, isolation, and absorption are the key factors in the liner.
The thickness depends on what type of material you use such as that duplex, egg crate foam, blackhole5, or lining it with fiberglass or polyester. I'd say generally no more than an inch.
Some pros are it absorbs vibrations, and reflected sounds in the enclosure and reduces standing waves that can cause distortion. It basically improves sound quality.
In a subwoofer, lining the walls has much lesser of an effect because the lower frequencies cannot be absorbed as easily. Some people use polyester fiber fill (stuffing) in subwoofers to affect the sound. I do know that people line the walls of their subs with things like egg crate foam, and even vibration dampeners, but I don't know why.
if it makes the box appear larger, would that not affect my calculaions to acheive the desired frequency. I made the box accordin to researching calculations and did not put insulation in mind, how much will it affect the outcome?
okay, so the question is, to insulate or not to insulate....
my box is 1.82^3(ported). that is what I wanted it to be. So I should not stuff it than? If I do the volume increases, that is not what I want right? What about the advantages it gives like absorbing higher frequencies, do I want it for that?
Is there anything out there that is similar to Blackhole 5, but does not cost an arm and a leg? I want to use it for some AV1's, but can't see spending that much on some insulation.
Viscous membrane sheets are really beneficial for damping 'live' surfaces like sheet metal/fiberglass/etc
There are generic sheets like Blackhole (Parts Express sells them) but IMO poly or acoustical foam is just as good. Acoustical felt is the finest damping material available (note that it's quite expensive)
I've never used WinISD so I can't comment...
Build the box according to what the program says, don't try to compensate for the damping with changes in the box size. Then fine tune the performance with damping material.
For ported designs I line the enclosure with a layer of foam or acoustical felt. For sealed designs I use .5-1.5 lbs of fill/cu ft. Then for either design, I add additional damping a few onces at a time. Everytime the bass will get tighter. When the bass no longer gets tighter, but only the overall output level drops, fall back to the previous amount.