I did not think about that.
You should simply be able to tell the scope to go to the object and it will do what it needs to do to get you there. If your handset is a 497 type or AudioStar, I think it may have that option.
If doing it manually, there will be a place overhead to the North (Oops, for you South) where you would have to be under the scope to see through the eyepiece. What I would do there is to rotate the scope around in the azimuth direction (now RA) so that the eyepiece is either on the east or west side to some degree.
I do not have the ETX 90, but do have an ETX 80. My scope has a 494 handset, which is not as smart as a 497 or AudioStar, but I might take it out and play a little. Mine does not have the ability to tilt to an equatorial position, so I would need to improvise somehow.
Anyway, it is an interesting question that I have not encountered before.