You might find that having the dogs their own seperate xpens and pee pads will help...If the alpha is the one having potty problems, it's because of behaviour and marking her territory and the other dog knows better than to mark over it so goes in his own spot. They need their personal space, even from each other so having their own xpen and their own crates to be in and their own potty areas makes it easier for them. If you can't do that, then as a last resort you could pick up a small vial of fox urine from a sporting goods shop a lot of vet's swear by this technique, spray just one tiny spray of it on the pee pad, usually the dogs will pee on it to mark and when they do that praise them and reward them especially the alpha dog. When you see the dog going anywhere else but on the pee pad, yell NO at her and put her nose to the pee so she can smell it..but don't rub it in the nose or anything like that because she will smell it an inch away from her face and know it...then lead her to the pee pad...lead her there, don't pick her up and place her there or she wont learn properly, lead her there playfully or with a treat and keep her there until she pees on it then reward her. After she's done that, let her play and clean the spot she peed or pooped on.
Does the xpen have a door? Do you use a pee pad holder? If not, I think its a good idea to get one because it will keep them from accidentally peeing on the floor, sometimes when they go on the pad it can seep to the side or get soaked in an area and leak onto the floor, or they play with it...the holder stops all this. Plus the holder has a certain feel to it they associate, and they can confuse just a pee pad with carpet. The xpen with a door is good, stick the pee pads in the xpen and let them out to play but make it clear to them if they have accidents off the pad they go into the pen. Make sure the pen has only enough room for bed and pee pad, that way they have no choice but to pee on it. You don't have to lock them up in a tiny crate to train them where to go. I use the Japanese indoor potty training method, it works pretty miraculously even with big dogs. It's much easier to train them, and is way friendlier than a crate. One side has toys and bed, the other the pee pad tray. They eventually learn to go where their pee pad tray is plus you can leave them there until they pee because it is caged in, then allowing you to reward them with treats and play time which works really good. Just to show you, this is the Japanese training method set up.
http://blog-imgs-12.fc2.com/p/o/o/po...i_suta-ta-.jpg http://image.space.rakuten.co.jp/d/s...e.46.1.8.2.jpg