How can you keep a female and male dog apart during her cycle?

The short answer is: you can't. He can smell her for blocks or even miles depending on his nose. He can smell where she's been and where she's peed. Stray dogs can (and will) actually track her back to your house. Proper management is critical. Keep them in separate rooms. Be aware that some dogs can figure out how to open doors. In such a case, put them in separate rooms with each in a crate and a carabiner reinforcing the door of the crate. Walk them separately. Do not allow them in sight of each other. Intact males can be extremely determined when a bitch in season is nearby. They can even breed through the wall of a crate given the opportunity. If they manage to get together despite your best efforts, do not attempt to pull them appart. During intercourse a gland on the male's penis swells while the female's vulva contracts. They literally become locked together (this is called a "tye"). They can be permanantly injured of forceably pulled appart. When they do come apart, take the female immediately to the vet. You have only 24 hours in which to take action. The vet can administer a "mis-mate" shot which will prevent pregnancy. Think of it as a morning after pill for dogs.