"Once you know where the problem areas are frequency wise, how do you deal with them?"
Depends on the frequency. Moving the speakers and listening position about can cure a lot of bass problems, but not all (for those you might need a parametric equalizer). Toe-in can cause/cure a lot of sidewall reflection problems (mids and highs). Carpets can cure a lot of floor reflection problems (mids and highs) and ceilings can cause problems as well but are more difficult to treat because of WAF.
Get your meter back out and create a base line measurement on your system as set up and then start moving things about again and see what physical changes affect the base line measurements (chart it all, don't think you will remember 2hrs later). Pick and focus on one frequency abberation at a time (I usually start with the bass). If you need help after you have flattened it as best you can, give a very exact description/measurement of your room, furnishings, speaker and listening position. I'm sure many here will be able to give you specific recommendations.
You mentioned that your speakers measured differently. Is this the room or the speakers? Have you reversed the actual speakers to see? Have you just reversed the channels to see if its the electronics?
FWIW, your speakers are just fine, and in many ways ideal but they do have limitations. If you accept their limitations you will lose a lot of angst about not having a "perfect sound" system. Just don't spend a lot of money trying to get them to do something they can't! Be happy and listen to all that great music! :-)