I agree with Beth. Barring from any health problems, it sounds like it's too much freedom too soon. At 6 months, Piper should be able to hold it for 5, 6 hours so your best solution is, if you're leaving the house, put her back in her crate and if you're home, make sure you can always see her so if you see her sniffing around a lot, you can take her out so she can pee/poop outside. If you have to be all over the house and don't want to lock Piper up in her crate, put her leash on and hook it to your pants so she has to follow you so you can keep an eye on her.
I agree a smaller crate works better but at this point she may have lost that natural desire to have a clean space. I would put newspapers down and gradually reduce it to just one newspaper. At her age she will still occasionaly have accidents. I don't consider them really reliable until about 1 1/2 or 2 years.
if she's not used to using pee pads, she's going to think it's a toy just as you mentioned. As others have said, put her back in the crate when you leave. When you come back, first thing: potty. wait until she's closer to being potty trained before giving her more freedom when you're gone. Set her up for success. Once you know shes a little better, when you're home, try a few times leaving her in the pen and you walk away into another room(out of sight) and see how she does then for maybe an hour. This can help her work her way back up to freedom when you're gone. Does she have accidents when you're home? Does she signal when she needs to go potty? Also, are the areas that she potty in in her pen cleaned with the cleaners that takes the smell away? if not, that may also be why she keeps going in the same place when you're gone.
Dogs don't mind that crates are small. I leave my dogs crates open when I'm home and often times they choose to snooze in their crates - even though they are completely free to leave it.