An SPL meter and test tones would let you know where you might need some EQ.
If you don't have a meter, you can do a little trial and error targeting the frequencies of the three axial (H, W, & D) modes of your room.
If you measure/convert the room dimensions in feet, these frequencies are calculated as 1130/(2 times the dimension). For example, if your room is 20 feet wide, the frequency of the possible node or null for that dimension would be 1130/40 = 28.25Hz. I would try something like -8dB at each of these three frequencies to see if you notice a significant change/improvement; then go back and fine tune whichever you noticed the most improvement from.
Although the PEQ allows you to add up to 6dB, this is worthless for a room mode. If your LP is in a null, adding SPL at that frequency will not decrease the null. You have to move the sub or LP for that (or add a sub).