There are two, 2bar MapV sensors. One is located on the hard plastic intake piping, pre-throttle body. The 2nd one is located directly atop the intake plenum. This/that is the one you want to swap out (with the new 3bar Mapv sensor). The one directly atop the intake.
You will absolutely need to install this if you're installing the methanol kit.
LMS does recommend installing the 3bar for some of their more aggressive tunes, along with the lower temp, 170 thermo. This, regardless whether you're doing Meth, or not.
I don't know what this secondary "box" is that you're talking about. A pic perhaps would help, as the one shoman04 put up isn't really clear as to wth anyone's looking at under there.

By the way you're describing it, it almost sounds like the same sensor I used for my boost gauge, as you're indicating it has the 3 wires, and the air line attachment.