You might look into zeutering the boy. I guess they stick a small gage needle into each testicle and put in a drug that causes swelling and the swelling and scar tissues will prevent anymore sperm from being passed, but the testosterone levels will be higher than if you did a complete neuter. They say they have results on dogs for up to ten years, but personally, for my dogs, I think I will pass. But then, I don't spay or neuter without a medical reason to do so.
Yes, keeping the puppies separate, once she shows signs of being in heat, actually once she hits 6 months, you better supervise interaction, because you can miss the first signs of heat as she will most likely clean herself.
The safest method would be to board the boy for three weeks, but who wants a youngster in a boarding facility for close to a month when they still need training and socialization?
If you cannot keep them separate, your best bet would be to spay your bitch around six months to prevent pregnancy. Puppies having puppies is just not kool. If you neuter or zeuter, remember that your boy, if sexually mature, will be able to pass viable sperm for about a month after the zeuter and days after a neuter.
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