i think it sounds like she's on the right track. 12 weeks is still very young. when i first got kash, he was 9 weeks old. and in the first month, i can only remember 3 times that he jumped off the bed in the middle of the night and pottied on the floor. after that he started sleeping through the night. he's 7 months old now and i've had no accidents in the middle of the night. he only recently started scratching at the door to tell me he has to potty. so you might have a ways to go for that part.
at first kash had free roam of the kitchen with ONE pee pad for him to potty on, but i realized after a few weeks of finding puddles of pee in different areas of the kitchen that he had too much space. so, i bought an ex-pen and put his crate, food/water, toys at one end and his pee pad at the other... he has not missed the pad since... and actually, in the last month, he has started to hold it all day until i get home to let him out. his pee pad has been clean/dry for awhile now. i leave in there anyway just incase. i'm still afraid that if i take it away, he'll start peeing on the floor. oh and one last thing... in the beginning i had to take Kash outside once every 45 minutes to an hour like you're doing. but now, he only goes once every 3 hours... sometimes i take him out too often and he won't pee... he'll just sniff around and i'll realize he just doesn't have to go yet!
anyway, i think you're doing well. keep it up, and eventually, she'll just get it.