Setup

What is the best way to setup my speaker system that I am finishing.

I am interested in the way I should go about setting levels, gain, and crossover points (3 way, 4th order active x-o).

Here is the equipment at my disposal:
TrueRTA
Behringer ECM8000
Rolls Mic Preamp
JustMLS
DMM

Also, is there an experimental way to find volume for calculating port length, or what is the recommended way, because I do not know the volume foam or glue or the drivers take up, etc.