I know I'm still pretty new to HBD, so there may be a way to do this I don't know about, but it seems like you should be able to re-order the draft prospects by individual positions.
For instance, Player A shows up as #23 overall prospect, and top first basemen. Player B is #29 overall and second first basemen.
If you value Player B more than Player A and therefore want to make him the top first basemen, you have to manually move him to #23, but that offsets all the other rankings. There should be some way where you could simply switch Players A and B, making B #23 and A #29 while keeping the rest of your rankings unchanged.