I have both a USB and 2 channel mic for measurements. I go to the USB one for convenience most of the time.
The issue with USB is you have no reference timing marker for measuring the "flight time" for the impulse, which will give you absolute phase information between different driver measurements providing for reliable phase integration for crossover modeling.
However you can work around this for USB measurements in a multi-driver system via the parallel driver approach and relying on drivers essentially being minimum phase devices (only works when using raw driver measurements as any components in the signal path may alter minimum phase behaviour).
The approach is as follows:
1. Measure tweeter
2. Measure woofer
3. Measure both tweeter and woofer in parallel
Make sure you don't change drive levels nor mic / baffle placement. i.e. ideally you will have both driver terminals exposed and just clip to the next driver to measure
4. Load measurement #3 into your simulator
5. Load both driver responses into your simulator and wire them up in parallel to the source / amp. Ensure you check minimum phase (derived phase) or extract this outside the simulator and load with the driver response
6. Increase woofer "Z" (acoustic offset) until the summed #5 response, aligns to combined measurement response (you loaded into step #4)
You now have a reliable Z offset for crossover simulation.
The downside is this is a single axis technique as Z will change off axis (the amount depends on the drivers / placement).
It would be nice it it worked that way.
Again THE problem is if you are using a USB mic with acoustic timing reference...that again is a 5KHx up sweep...phase and resultant timing delay estimation is bogus for any driver not playing into tweeter-ville.
Try this... take transfer functions of the driver sections with hp or lp in place, above or below the intended pass band, as fits the driver.
Watch how the phase curve changes, and estimated peak IR time changes.
If you can, use linear-phase hp and lp. And let the light shine