Mike has a pretty detailed summary somewhere, I just can't recall what thread ....
In a nutshell, do one channels at a time .. start by taking a speaker measurement and determine the -6 db point of the speaker
Do a measurement of the sub on it's own for that channel, try and match the -6db point.
Do a measurement of the speaker / sub combo and see if they bring the -6 db point up to flat take it down further... dial in the phase to eliminate cacelation if any is present... some placement alterations may also be necessary. You can use the PEQ to deal with a major node/null.
Repeat for other speaker/sub combo
Tweak from there
jay