Rudy, I've been thinking ahead to this problem, as I have ordered a set of ALK ES filters for my two LaScalas.
So far, I've come up with two approaches.
(1) Use REW just as a signal generator. One could use the pink noise generator to cover the heart of each driver's response while avoiding the crossover, in my case, for example, 60Hz-450Hz for the woofer, 550-3900 for the midrange, and 4100-16000 for the tweeter, and measure each with an SPL meter. Then adjust the midrange and the tweeter so they give the same SPL measure as the woofer.
(2) Do full range measures of each speaker individually, with Audyssey Off of course, in the middle of the room as far away as possible from the walls, with the mic placed near field facing the speaker. By looking at the graphs, one could try to adjust the midrange to match the woofer in level, with no weird anomalies around the crossover, then do the same to match the tweeter level to the midrange.
I have no idea how well either of these techniques will work. Hopefully someone has already tackled this problem and can share his or her insight.