Bryan, as Michael said, the most common configuration is to set all speakers "small" with an 80Hz crossover between them and the sub. Now, if you've used the automatic setup that your 990 has, it may have made different settings, in particular it may have set the M60s "large" because of their good bass response. Despite this, since your EP500 is even better in this area, you should manually use the small/80 setting. Since the 990 allows for different crossover settings for the different speaker groups you might want to try 100Hz for the QS8s and/or VP150, but a uniform 80Hz setting might be as good as anything; experiment.
As far as the setting of speaker levels and distances, the automatic setup that the 990 does can be relied upon to do that accurately.
By the way, on your other question, use the spikes if you want to have the M60s more firmly set into the carpet, but there's no discernible effect on the sound involved.
Enjoy the music, not the equipment.