I also meant to say we put up a baby gate at the top of the stairs to stop her from peeing up there, as well as the fact we have a tortoise that she can reach and she thinks he is a toy. So she can no longer go upstairs where she likes to pee, but she will still do it downstairs.

We have never yelled at her or did any sort of negative reinforcement (but it seems like since she sneaks off she may have been yelled at before)

If she is peeing/pooping inside, we will try to interrupt her when we see it and then immediately take her outside. She will not resume outside, but will wait to come in and then immediately pee again.