Measure the Inches from the driver to your ear. Thats only the first step. Before doing that, make sure your right and left RCAs are correct, some people mess up and their left and right sides are switched.
After you enter the initial inches, Mute the sub and tweeter, then work on the midrange. You can choose either the left or right side values, you just need to subtact or add and actually see how the sound stage shifts left or right, to do this, you'll want a centered vocal track, for example, echosmith- bright. When you hear the vocals directly dead center right under the rear view mirror thats when your time alignment is centered and proper. Now turn off the mids and do the same thing with the tweeters.
Make sure your speaker level values are zeroed out. Sometimes when you initially set the listening position to front left, pioneer has wierd @ss speaker level values that attenuate the right side.
Auto time alignment and EQ is complete trash lol totally off center and the auto EQ fks with everything and will clip the sh*t out of your setup.