Well, I was going to suggest that you create an Auxillary Dictionary and then add your acronyms to it (not perfect, but neither is Quark).
But, as I went to setup what I thought was possible, it appears it is not (at least in my Quark 7). Keep getting error "The auxillary dictionary is damaged [55]", even though I just created it and there are no entries in it yet
I don't know why it is that Quark seems to be going backwards and things just don't work or behave the same way they did for the First decade of Quarks release (you know, the good old days when Quark was king of the hill?)
In version 7 and now 8 also, the program is just a shell of what it used to be. Can't run the good-old 4 or 5 anymore (thanks to Apple and the death of Classic/OS9).
Quark should have left some things that don't need improvement alone! I used to think that the spell check in versions 3-5 was poor, but it was at least manageable.