Hi Pekemom, as you can see, I'm also a Peke owner and I'm a HUGE Peke aficionado. I used to mentor with several renowned Peke handlers and breeders, and I'm still madly in love with the breed. First, I noticed that you mentioned breeding. Because I love this breed so much, I have to ask: Are your pups being shown or do you plan to show them? Or are they being worked in the obedience or agility or similar ring? In other words, are they being proven? The reason I ask is because there are a LOT of homeless Pekes out there, almost all due to unnecessary breeding. If you are showing the dogs and everything, kudos to you! And if you are showing, who'd you get them from? I may know the breeder! But if your pups are solely pets, I highly encourage you consider neutering and spaying them. At this point in time, there are just too many homeless Pekes out there to encourage breeding JUST for producing pets.

Re: Potty training. Take it two steps back and use the tether method (keep a leash on her and tie it to your waist). Since your female has gotten used to peeing where she sleeps, you can't use that natural deterrent anymore. So, rather, you'll have to keep her by your side and take her out everytime you see her sniffing. This tether method makes sure that you won't miss a signal.

Re: Female's dominance over the male. It's actually very common for the female to dominate the male, especially in unaltered dogs. I try not to mess with the dog's pecking order too much because too much human intervention can do more harm than good. However, to reassert yourself as THE one and only leader, I also recommend NILIF: http://k9deb.com/nilif.htm
Especially in regards to feeding, I would try "cooperative feeding". In other words, have both female and male sitting in front of you. Give the female a treat while simultaneously giving the male a treat. Then give the male a treat. IMMEDIATELY treat the female thereafter. A clicker works wonderfully for this. Repeat this enough so that the female regards you giving resources to the male as a good thing. And if she ever gets too rough with him or if she starts to border on bullying, take a can of pennies or use a very low, loud "NO!". And then redirect her to her toy or her bed or her area, whatever. Just remember: whenever you punish, you have to immediately follow up with a redirection. Good luck!