A complaint of mine too, in that it's so difficult to do this correctly. Anyway, from some code I have, there is a line like so:
set_location_assignment CLKCTRL_G4 -to "toplevel|...:sii_clkctrl:clkctrl"
I took out the middle of the hierarchy, since it's someone else's IP, but hopefully that points you in the right direction. I assume you're explicitly instantiating the altclkctrl block, which allows you to name it and therefore control thename to tag the assignment too.
Another idea, although not positive if it will work, is to make a copy of your fit project and then back-annotate it to the routing level. Look in the .qsf for similar assignments and then cut-and-paste them into your design. Not sure if that will work.