When you think about it the right way the idea is fairly simple :
Here the "Free topos" means the "object classifier", that is the classifying topos of the theory with just one sort (one type) and no axioms. A Frame in this topos hence corresponds to a purely propositional geometric theory on top of this theory with one sort and no axiom, so you end-up with exactly a geometric theory with a single sort and as many propositions and geometric axioms as you want (so in particular, you can emulate function symbol using functional relations).
So frames in the free topos corresponds exactly to one-sorted geometric theory (with propositions and functions). In practice any geometric theory is (Morita) equivalent to a one-sorted one, so you can describe any theory like this. But the presentation as a frame in the free topos depends on what you chose as this sort.
I do not know a reference that present things exactly this way. But if you look in P.T.Johnstone Sketches of an elephant, you should find a good approximation to it as Theorem D3.2.5. The theorem might not be exacltyexactly what you are after, but it contains all the key elements. (Also using that localic geometric morphisms corresponds to internal frames of course)