I sometimes find myself caught out slightly when switching between my regular Pentaprism SLR and waist level finder on my TLR, especially when carrying them both to photograph sports. What seems to especially get me is adjusting level on the TLR, as I'm prone to both rotating the wrong way, and then promptly over-correcting my error, because why wouldn't I make things harder on myself in such cases?
However for the most part I don't find it to be that bothersome, and consider myself lucky to be able to quickly switch between my SLR, TLR, and large format view camera. I find the key is to slow down and make small slow adjustments to start with till my brain clicks over to the different view space before trying to move quickly.
And when tracking with the TLR's waist level finder I tend to try and visualize where I am in the space as much as I am looking through the viewfinder - Kind of picturing it as if I'm looking down on myself from behind, and rotating from the waist to roughly point the camera in the direction of what's going on. I'm sure the volume of video games I've played over the years has warped my mind's ability to process spaces in interesting ways.