You're doing it the way we do (except for the getting up every 3 hours part), and it sounds like it's going good. We don't use a crate in the potty training process, except for them to sleep in at night. Since she's finding the pad in the expen, I don't see any need for the crate, unless you were trying to train for outside only.
You are teaching her to wake up every three hours. If the crate is next to your bed on a chair, or something that raises it up to a good height, I'd wait for her to wake you up. She will stir, or spin, or scratch, or whimper when she needs to get out to potty.
She will smell the pad under the grate. I'd let her pee on it once, and then put it under the grate. Make sure the box stays in the same place for now.