She will! She'll get accustomed and you'll start waking up in the morning to see her staring at you. When Banjo was small and stressed, she'd climb her trees. I admit that I dug her out sometimes and I regret it. Burrowing is a-ok. It's like she's arranging the furniture to fit her personal style. When she knows her fav holes won't be disturbed, she'll likely come out more, knowing she can retreat whenever.

Did you put in any new decorations? Sometimes they can have a chemical smell even after being washed and it can bother the toad. If not, then relax... she likes her dirt.