[Sunnie]

12 weeks is really early to be concerned too much, you just need to be consistent. It is confusing for them to be trained to go outside and at the same time to be trained to go inside on potty pads. I struggle with the same thing. Mine go outside 95% of the time, but I still keep some pads both upstairs and downstairs and they occasionally use them as well. When using the x-pen I used a vinyl tablecloth or shower curtain to protect the floor or carpet, then put the crate in one corner, potty pads in another, food in another and a play are in the last corner. When my babies were smaller (birth to about 8 weeks, I always kept a sheet covering the top to keep in the warmth. I just used clothespins all around. Then I took off the sheet, but it wasn't long until Rainbow started climbing out. She didn't even have to use the crate to get out.... she climbed the corners while poor little Beamer sat there and watched but couldn't figure out how to do it himself lol. So I started putting the sheet on top again with the clothespins and she no longer could climb out. I didn't let the side hang down because I wanted it to appear open to them so they could see everything going on in the house. I just folded the sheet so it fit and pinned it with clothespins and it worked like a charm.
Sonya