If you are using YPAO or other room correction, the phase and timing issues are generally done for you. If the bass is boomy you may need to play with the XO on the avr, avr and sub. There most likely is a bass bump around the XO. PEQ is one of the easiest ways to correct this type of problem It can be difficult to get the roll off of the main to blend with the XO . Phase changes has frequencies are lowered. The system has an absolute phase and a relative phase.
Klipsch RF 7 based HT 7.4, Pioneer SC 35, Acurus Five 200 amp, Chase SS 18.2(2), VS 18.1(2), Samsung BDP F 7500, Asus/My Book Live HPC 4 TB
Yaquin VK 2100 amp, McIntosh XR 5 speakers, Samsung BDP F 7500