http://dictionary.reference.com/browse/in+bad+with,+be I've never heard of it (in the UK) but it looks like it is an American expression - see link. We need an American to tell us if it is in current usage. The definition in the link only relates to your first example, not the second. For the second, you can say :"I tried not to get on the wrong side of Wally."

"In bad with" doesn't make sense. If you're wanting to say "be disliked" or "be out of favor" then it would be something like "be disliked by" or synonyms for "out of favor" like shunned, unwelcome, unwanted, or unaccepted. For your sentences I would probably say something like the following: She was afraid she'd be disliked by her new supervisor. I tried not to get in trouble with Wally. We disliked each other from the start. OR We misbehaved with each other from the start. -Depending on what meaning you are looking for.

I have never heard this expression. I would say "on bad terms with somebody" or the other expressions you used,out of favour etc.Those are fine. She was afraid she'd be disliked by her new supervisor. I tried not to get in trouble with Wally. We disliked each other from the start. CORRECT We misbehaved with each other from the start. -Depending on what meaning you are looking for. This is not the same meaning.THis means that you did bad things together not that you had a bad relationship. You can say we did not get along from the start.