I second Cford and would add that cutting is much safer than boosting signals.
An equalizer not only alters phase but cuts your primary signal coming out of the speaker and therefore all the signal you hear (including the reverb, secondary or room modes); therefore it should be used sparingly.
Cutting the primary signal to achieve a flat combined response will leave the primary signal at a lower level than normal compared to the rest of the primary sound (which will be farly flat across the frequency spectrum if your speakers are any good).
Therefore equalization is probably best applied to only the very lowest frequencies...where your ears/brain are less able to distinguish primary from reverberant sound.
Acoustic treatments should be preferred as they affect the reverberant sound only, however, it is very difficult to tackle room modes below 60 Hz without using extensive treatments and even rebuilding the entire room....so an PEQ is a good practical solution in this case.