I am wanting to attach a seat on top of my bench seat on my 12 ft Jon boat. Problem is I can’t bolt anything because the seat is full of foam underneath. Any suggestions?

Threadserts also called rivet nuts

Clamp on for boat seats.

https://www.amazon.com/Wise-8WD14-Boat-Seat-Clamp/dp/B001RPBIN0

Those seat clamps can hurt you and cause all kinds of bad things unless you run all-thread or bars through the seat to hold them.  When you lean over sideways to get a fish, unhung or something they flip over to the side, causing you to start grabbing for something to keep from going over the side.  If you have something like your rod in your hand, you can drop it in the lake while your trying to catch yourself.

If you want something permanent, you can try rivnuts.  Since I store my boat upside down on the trailer, I want mine removeable so I bent a piece of sheet metal about a foot wide that's bent to slide over the bench and has winged bolt that screws into a hole I drilled near the bottom of the bench to keep it firmly in place. 

For the rear bench, I installed the slide rails that let you move the seat to the side to run the motor.  http://www.boatstoreusa.com/seating-pedistals/seats/chairs-stands/swivl-eze-by-attwood-sp15900-tilt-n-slide-jon-boat-seat-brk/?gclid=EAIaIQobChMI_rnP05nJ3AIVmLjACh0i6QUWEAQYBSABEgKVPvD_BwE.

The 15" are a little too short for my likings.  I prefer the 30" slide rails, but they are a little harder to find.

I turn the piece that goes to the back around and sit the mount on it rather than under it.  Makes it a whole lot easier to move to the side and remove, and still holds the seat just fine.

Academy usually has them and are about as cheap as anyone.  It will also work for the center bench.

One note I will mention.  When drilling and mounting seats in the top of the bench that use a small area like those swivels under the seat, the aluminum is pretty thin and tends to crack or let the screws/inserts pull out from the constant flexing caused by the weight from sitting on them. 

Thanks for the replies! I will definitely look into to all this