Group booking in L & M fare classes: Can I split off my PNR and/or upgrade my seat individually?

I am leading a study abroad trip with myself, a fellow faculty member, and approximately a dozen students. We are at the flight booking stage of our preparations and the process is different than they've been in the past.

For background, I do not book the flights myself. Instead, our university uses a third-party travel arranger to organize flights. In previous years, I've been able to have the arranger book my ticket separately, thereby giving me my own PNR. This year, however, I'm being booked in the same transaction as everyone else, which I presume means we'll all have the same PNR.

I like having my own PNR because I can upgrade to an extra legroom seat or a higher class of service. However, I'm anticipating that our outbound flight will be booked in the L fare class and our return will be booked in the M fare class, both of which show the ominous message "Seat: Assigned at Check In" on the PDF the arranger sent me to review. As a tall dude who's approaching 40, the idea of getting stuck in a middle seat in front of the rear galley sounds awful to me.

Once the flight has been booked, what opportunities, if any, will I have to split off my booking into a separate PNR and/or pay to upgrade or select my seat individually?

Both flights on AA metal, not codeshares.

Thanks!