Look up the frequency response specs on your front left/right speakers then set the crossover for those speakers 10Hz higher than the lowest frequency they are rated for (or set speaker to "Large" if receiver only has this option instead of a Hz setting). Turn off or unplug all other speakers then play your typical type of preferred music at a level as high as you would ever want to listen to it. If you find they're distorting from the bass and can't handle the material raise the frequency cutoff until you find the speakers are playing cleanly (or set speaker to "small"). Many 5" equipped speakers can handle a 80hz cutoff but it should be checked.
Once you've got that set do the same with the center speaker (if using).
Finally add the sub and when it's level matched and you've set the frequency cutoff for it to the other speakers try reversing the phase on it to see if it sounds better normal or reversed (if you change the subs location you'll have to redo this every time). You may want to play around with sub frequency crossover setting once everything else is done as things may now sound different.
Then when you're bored you can play with speaker width, then toe-in, then change all the settings all over again and so on