What ever flotation you remove, you need to replace.
I cut open the seat bulkheads in my jon boat, rolled the edge over 3/4", then lined the entire compartment with 2" sheet foam. The foam block inside the bulkhead had more volume than what I put back into the compartment, so be aware you may need to do multiple layers of 2" foam, double bottom, double sides. FWIW, the foam block inside the bulkhead was surprisingly smaller than what I thought was going to be in there. I installed foam lined decks, so even though I have less in the bulkheads, I have more total foam in the boat.
Don't go hacking a hole into the compartment until you know how big the opening needs to be. I cut twice, once to figure out the size of foam block and remove it, then cut a second time to the actual dimension. Also, you must roll the edge over, or the top of the seat bulkhead is going to be very weak.
Here's the best pic I have, of how the foam was installed.