Depends on what you want to replace it with. if you want to use the polystyrene stuff it's as easy as cutting boards and stacking them in the cavities. BUT the manufacturer didn't use that because if you spill gasoline on it it will dissolve. Pouring urethane isn't too bad. It's a 1:1 mix, so you take two Solo cups, fill them to the same line, then pour one into the other and stir...then dump the mix in the boat once it's uniformly mixed. The trick is knowing how much it will expand, but if you're doing it one cup at a time you'll be fine. Takes about 20 minutes before you can pour over anything you've done already, so if you start with one cavity, then pour the other two you should be just about ready to pour a second batch in the 1st by the time you've done the other two. Trick is to keep the foam from seeping out when it's in it's liquid form and to build-in some design to allow the boat to shed water back to the transom drain (probably how the boat originally became water logged.
I had mostly positive results using duct tape to seal off cavities so the foam couldn't run out. It's fairly tacky, so it isn't like you're trying to contain water. Once you got toward the top of the compartments you'd want to take a piece of plywood that will cover the cavity section you're pouring, cover it in plastic (garbage bag works nicely) and after pouring the last of the foam place the board over the top of the cavity and weigh it down with cinder blocks along all the edges. Some foam will blow through, but once it hardens you can break it off. If you're using a thinner decking material the important thing is to have the foam flush to the underside of what will be your deck so it can bear the load. The foam is 2lbs per cubic foot, so it doesn't add much weight and it allows you to use thinner decking materials and save on weight/cost. I think there are progress pics on my build thread.