"Do you remove the male mice when the females are ready???"
NO.. once you setup a colony.. say a 1.4 group you leave them together for the entire breeding life of that colony.. you NEVER remove males or females, and adding in new females can sometimes be difficult.. NEVER remove males.. it causes all kinds of problems..
"I had two or three females ready to go, checked a few days later, they birthed and ate them all. Is this always the case if males are left in????"
Were they firsttime breeders?.. If they were, thats the answer right there. First time mouse mothers are more often than not HORRIBLE mothers and kill their litters. By the time the second litter comes, shes calmed down enough to figure it out and takes care of them.
Also.. how often were you looking in on them?.. Mice stress quite easily, and dont like people constantly peaking in on them. I found out that just leaving them alone, and only messing with them on cleaning day is the best policy. 
What are you feeding them?... low protein diets cause moms to eat litters also.. 22-23% is optimal! 
"In my rats they actually help out, bring the females food and move the pups to the moms when they stray."
Rats are a whole diffrent ball game than mice, how you setup colonies, and the whole breeding process is so much easier with rats.
Male mice do help raise offspring just like male rats do, so thats not an issue.
best of luck
dan