To be honest I have never actualy used GPS on a cleanflight controller, as all my cleanflight drones are for FPV racing, so I dont use GPS. All my GPS drones are larger ones with gimbals etc and all run Pixhawk.
But I am pretty sure that you need to have baro, mag, and either acro or horizon mode enable together with either one of the GPS Hold, or GPS RTH features.
When flying just make sure you first test GPS hold before RTH to make sure its behaving as it should. Worst case if it does start to act weird you can just switch back to acro or horizon mode on its own.
However that said, the GPS modes are still in early stages with cleanflight but should be ready in the next, or in one of the next releases. You can keep track of it here - https://github.com/cleanflight/cleanflight/issues/197