We have just V and JV, but we run them together for a few weeks when we are waiting for winter sports athletes to merge in and then while making decisions on squads. It is really tough. No matter how many stations you set up or how well organized it is, there are fewer quality reps and it takes too much time.
While I agree with Ironhorse that it can be good to combine AT TIMES, I think he missed that you are combining Frosh/Soph and not the V team or coaches so most of his PROS list does not apply.
Also, 3 coaches total for 35 kids across two lower levels is really short-changing the kids at a time when quality attention and instruction is most important.
I would suggest doing everything possible to get a few additional volunteers to help with the program. If the school is big enough for three squads, the area should be big enough to mine for some extra help. Talk to the local college or JC for recommendations on young players just out of the program. Perhaps there are HS grads in the area that were good players and are still in the area and available to help. Even if you have to get help from a (gasp) parent with decent credentials. No team should be run by just one coach, particularly Frosh/Soph where the players are less likely to be able to run their own stations effectively.
Then, schedule a good rotation for use of the baseball field, football field and cages, so that each squad gets fair share time. Cage time may also require coordination with the V squad if possible. I know that other programs in our area with three squads do it this way. With a little extra help and good planning, you should be able to maximize practice time for each squad more effectively than running 35 kids together for a whole season. JMO.