Now that you have calibrated your measuring system, it's time to calibrate your sound system. For this, it is better if TrueRTA is running on a different machine than Media Center, but it can be done if they're running on the same machine.
You will need to get a WAV file containing a special kind of sound called "pink noise". Pink noise has a specific energy distribution so that when you play pink noise into an analyzer like TrueRTA, you should get a perfectly flat line. To find a pink noise wav file, do a google search for, "pink noise wav". You should find one out there somewhere.
Note: DO NOT USE AN MP3 OR WMA FILE OF PINK NOISE. Because MP3 and WMA compression change the frequency distribution of the sound, they will throw off the results. Only WAV will work. Okay--or APE, since it's lossless.
Interesting Thought: However, if you always play back WMA's or MP3's encoded in a certain way, you could encode the pink noise to a similarly-encoded MP3 or WMA, then tune your system with that noise. This would allow you to compensate somewhat for the changes in frequency distribution caused by the encoding.
Set up the microphone at your listening position. The microphone should be pointed straight up, not pointed at the speakers. It is best to do this with a mic. stand, but if you must hold it with your hand, you can. Play the pink noise in MC, with "repeat" turned on. Start TrueRTA. You will see the frequency distribution of the sound coming into the microphone. Now, if your system and room were perfectly flat, then you would see a flat line on the analyzer, but that's not going to happen. Your speakers will amplify certain frequencies, your subwoofer will be turned up too high, the drywall in your walls will reflect certain frequencies, etc... etc...
Your goal is to get that line as flat as possible. The best scenario is if you have a dedicated standalone equalizer, but many people won't have that. If your stereo or receiver has an EQ built in, you will have to decide if you want to use it. Typically, these EQs aren't very good, sometimes only having three bands (bass, mid, and treble). If that's the case, I recommend that you set the EQ in your receiver/stereo to "off" and tune within MC.
First, if you've got a dedicated subwoofer, balance that with your main speakers. Play with the subwoofer's level and crossover settings while watching the frequency response. If the crossover is set too low, there will be a "valley" between the higher frequencies of the main speakers and the lower frequencies of the sub. I recommend that you turn the sub's crossover all the way down, then turn it up until that valley "fills in" with the main speakers' frequencies. Then set the sub's level so that it is approximately equal to the main speakers' level (e.g. the lower frequencies are the same height on the graph as the higher frequencies).
Look for peaks or dips in the frequency response. On the X axis, you can see what frequency those peaks or dips are at. Find the closest slider in MC's equalizer plug-in and move it up or down. Keep doing this until you have achieved the flattest response possible.
Note: you've got two options, by the way--pull down the peaks or push up the valleys. Sometimes, a valley will be impossible to fix with MC's EQ, but pushing down the peaks to either side of the valley will work fine. And vice versa.
Listen to some music. Turn the EQ on and off. Smile at the amazing difference!