Reserve drone comb to add to honey supers during the flow period. Drone comb stores honey beautifully. You will want a good honey cap below to prevent the queen from finding the drone comb and just making more drone.
The required grading / sorting of comb is a undisclosed downside of "natural" comb systems.
Best solution I know is to keep two or three boxes on your tailgate and sort and label as you inspect.
I find a deep + medium design works as a natural sort -- Edit the deeps so they are a well organized and balanced broodnest (honey>pollen+drone>worker cell working in from the outside). And let the mediums represent honey supers. When you want a broodnest grab a deep with the confident knowledge, that you have a balanced nest.
The argument that deep brood is "too heavy" is simply not true -- as broodnests are featherweight compared to honey. The argument that all-mediums standardize equipment is misleading, as detailed above -- you have to sort individual frames in an all-medium system. In a deep + medium system the sort is by box, not by individual frames.