If you're driving and you say that you are going to wait here then that means that you are going to stop at your current location for a period of time.
If instead you say that you are going to wait up (t)here (at a location) then that means that you are approaching the location where you intend to wait. Wait up here would be used for a location that was close, wait up there for a location that was farther away.
The difference is between a location you currently occupy and one that will occupy in the future.
To confuse things further, suppose that the phrase only read wait up, and was used as an imperative. In that case it would mean that whoever you were speaking with wanted you to stop and allow them to get to your location before continuing onward.
Example: John and Emily are driving in separate cars, searching for their friend who will be leaving school soon, but they don't know exactly where their friend will exit the school. They are talking on the phone. Emily is far ahead of John.
- John: Wait up Emily, I can't even see you anymore.
- Emily: You're too slow. OK, I will wait here at the southeast corner of the school.
- John: OK, I'll wait up there at the northwest corner.
- John asked Emily to slow down or stop so that he could join her.
- Emily has already reached the location where she intends to wait for their friend, and let John know that.
- John told Emily where he intended to wait for their friend, though he had not yet reached it.