I get the spots sometimes, too - they are not permanent and I find them much more in my cold wash loads than my warm or hot loads. If I see one, I just squirt a little pre-treat on it and re-wash in warm and they disappear. I make my own laundry soap now, but have had the spots no matter which laundry detergent I use.
As far as separating, I do a dark (black/dk blue/red) cold load, a warm load with socks, jeans and towels, a mixed load with multi colors on cold, and a cold white load. When in doubt on a color, I always wash it with some jeans or colored towels the first few times. After that, I throw it in the mixed cold load. Yellow is a tough one :) If it's light, it goes in the cold white, if it is dark yellow, I put it in the mixed cold. If I can't decide, I wash it with my yellow towels the first time in case it bleeds.
Good luck!