You need two quality TEs to be effective with it as a primary offense, so you need to have 3-4 TEs on your roster. Running the bone means more RBs, and running trips or shotgun means more WRs. You can try to even the bench players out over all your offenses, or (at least at the DIII/DII level) you can just shift from one primary offense to another as your recruits mature, i.e., recruit 2 TEs one cycle, 3 RBs one cycle, 3 WRs one cycle, then as they get ripe, run the box as a primary when your TEs are SRs, run WB as primary when your RBs are ripe, and run trips/shotgun when your WRs and/or QBs are ready.
Generally, the only drawback to running a position specific offense is that you can't always find prime TEs exactly when you need them. I try to use either PS or the I for a primary, and add in more box, bone, trips or SG depending on my experience and depth.
You can't really do this at DIAA/DIA (or at least I haven't), because you need more formation practice, so changing your offensive system on a seasonal basis means you can't be as efficient with your practice time.