In my experience, squeaking is good...squeaking makes babies, yis yis.
When I'm breeding, I keep the girl(s) with the guy until I know she's preggers. I usually pull the girl out and put her in her own shoebox tub when she's ready to pop, but that's my experience, your mileage may vary. =)
I haven't had girls kill a male before tho...could just be "i don't recognize your smell, you don't smell like us" squeaking and nipping. If he lasts a few days, he'll get your colony's smell and then should be good.