i had a box for mine that sit flush up top where the t top bag goes and went all the way down to the well, i then bought a box that didn't go into the well but sit flush on the edges before the well and it sounded way better than the other box. i just got my stereo stolen and im putting a new one in and i'm going to make my own box and just wanted to know what is best, i would pefer 3 10's but probaly 2 12s. what sounds best

 

Whether the box goes down into the well has absolutely nothing to do with how the subs will sound. The subs themselves, the airspace in the box, the tuning of the ports if it's ported, and to a lesser extent, the position of the subs, will all have an effect on the sound.

The shape of the box will not.