You would only notice phase when measuring both sub and speaker combined as a full range sweep. Try a measurement running sub and speaker together now.
The other way to get a theoretical full range is using the alignment tool to combine the sub and speaker measurements together. To do that, click "ACTIONS" button on the right side, then click "ALIGNMENT TOOL". Set the two selections to Left Speaker and Left Sub and see how the stack up. If you have phase cancellation issues, it'll be a massive dip near the crossover point. You could also click the cursor at your crossover point and click the button "Align Phase at cursor" and it'll tell you if you're off a bit so you can adjust and re-test. Remember, phase knob on subs ADDS delay to the sub timing so if it's saying your subs need negative delay, that means turn down the phase knob.
Hope that isn't too confusing, but that fiddling has really helped my system.
-Lloyd