If you are using Keyclone - then under the command section there is an option to set CPU affinity for each clone. Set it once and you are done.

Additionally, I would set MaxFPSBK to 15 and MaxFPS to 40. That will really reduce the burden on your machine.

Some tips:
Get an addon called AutoAcceptInvite - it will allow you to set your Alts so that they will automatically accept invites from your main. Next creat a macro:
/invite Alt1Name
/invite Alt2Name
/FFA

Hit that when you start, then hit it again. It will create your party, then set loot to Free For All.

When you get a collection quest, run the main to the side of the mob and stop - this will put the alt just in front of it - then mouse over,right click... done. I found that trying to run straight up to a mob put my followers too far behind to loot, so then I'd have to steer them up to the loot manually. It works much better to just get in the habit of running up just to the side

I 5 box with 4 on one screen and 1 on my main screen. I always start with the same toon on collection quests... finish with that toon then move to the next. I finish with my main last because that ensures I always see the "sparklies" of unlooted quest items.

Welcome to multiboxing