Just add it as the last plugin of your master but don't forget to take it out when you bounce your file. Using the new Geq from waves might be advantageous in this, as the modern mode offers true plateau control that is not additive and is not using proportional Q filters. At that point, if you're still not satisfied you can always fine tune the room with using pink noise and a frequency analysis program, like rew 5 and others. Then use bass traps, broad frequency absorbers, diffusers to control the frequencies and flutter echoes. The only way to correct those is to modify the geometry of your room not to mention that size will also have an impact on that. Also, as it was probably mentioned already, if your room is not treated, tuning the room will not change the standing waves. You'll want to use a pink noise as it has a fixed equal power throughout the frequencies. Those were the days when "digital" meant "wristwatch" I should have remembered that white N pink both have all freqs - we used to do live sound w/ a white noise analyzer and one cheap 32 band graphic eq to flatten the room. I knew it was time to analyze the new room when a 4 inch change in my head/ear position caused the bottom to drop out precipitously from the mix for no other reason. I also moved from a nearly perfect small EQ tuned room to a much bigger cave like untuned room. I've put off dialing in the room for months because I'm a 2 bit lazy audio engineer. Be methodical and do more research as needed.
My solution is to dial the subwoofer so that it fills in the hole, right at my mix chair(I turn the sub off if I have a producer on the couch as the sound is flat on the couch WITHOUT the sub(a reasonable tradeoff ). In my room, I had no option and sit almost dead center(the worst spot:o:o). IIRC, the ideal listening position is 38% away from the front wall(adjust according to the front-to-rear dimension). To get help here, you need bass trapping and/or to move your setup. You may also find a couple that are way hotter. In the average room(let's say, a spare bedroom with most any 8" monitor) I would expect to find at least 2 frequencies that are way down(like 12 to 14db softer) than the average volume. Use your ears(and, if you have a flat mic, use that to help support what your ears tell you). Be patient and take lots of notes on lots of frequencies. Sweeping down is likely to reveal some serious imbalances which will likely start just below 200Hz. Inaccuracies in the upper range could be due to reflections off the walls, ceiling, desk top. Slowly(very slowly) sweep up and take notes on any frequency that sounds either louder or softer(with luck, it should be fairly smooth going up from 500Hz).
Start at 500Hz(really, anywhere is fine, but you need to start with a volume that is loud enough, but too loud(around 85db). With this, you sit in your normal mix chair and use the sine wave.
Without that level of measurement, my next recommendation takes a little time and some good old "analog" help(namely a pencil and paper:D). It covers the typical RTA function, but on steroids, and allows for accurate phase and time delay adjustment(my subwoofer is fed from a digital crossover with custom filters to create an asymmetrical slope and to time align the sub to my main speakers). I happen to use SMAART Live with a measurement mic.
Pink noise is great, if(and only if) you have an accurate analyzer of some sort. My 2 cents relates to sound accuracy, not volume.