The rear compartment of my boat is really tight.  The guy that had the boat before me did not use anything to secure the batteries.  That is not sitting well with me.  Problem is the only place to really secure the trays would be into the hull.  I am a bit hesitant to put screws into that.  I am thinking about using some 3M 5200 to glue them down.  Thoughts?  Ideas?

i screwed mine down.

you mean your "hull" hull?  As in through the bottom of your boat?  Fiberglass or metal?  If its thick enough fiberglass you could use really short screws that would probably work OK.  Either way I wouldnt risk screwing down through you hull just for batteries.  If you dont have any other metal to screw it to, I would try the glue or possibly screwing them all to one piece of wood that is just long enough for your compartment, then you could stabilize that some other way.

Question, what would you do if you need to replace a glued down battery?

I thought he meant glue down the battery holder.  You'd then use the strap to keep the battery to the holder.  You'd obviously have to not glue the holder down through the center section so as your strap is free to move as needed.

Are the batteries sitting on the hull?  If so, I would not put screws into the hull.  It's not very likely to be thick enough, and if you use screws short enough, they'd lack the holding power to keep a sixty or seventy pound battery in place when the boat starts bouncing around.

It's impossible to tell you how to do it without knowing the construction involved.  Most boats that have compartments have a plywood deck above the bottom of the boat.

Need to know more about the boat.  Pictures would be helpful too.

Yes there is a small removable platform that covers the livewell and bilge pumps.  There is room to "screw" one battery tray down there and still have relatively easy access to the bilge pump.  The other two are going to have to sit on the back corners of the actual hull.  Like mentioned I am very hesitant to put short enough screws as I would feel comfortable as to not go through the hull.  Then I would not be comfortable enough in those short screws to have enough bite to hold down a size 29 battery.  The more and more I think about this the only viable option is to glue them down.

I would love to know if the previous owner "upgraded" the gas tank.  It has a 33 gallon!!!! tank in an 18.5 foot 115 hp boat.  It really tightens things up back there.  I will see if I can get a pic.  Right now its pushing 100 degrees, the boats covered up, and the AC is feeling pretty good. :

If the boat is a bass boat, usually the left and right side of the bilge area is covered floatation and is more than 6" higher than the boat bottom (where the bilge pump is) and a flat surface unlike the exterior of the hull which is probably slanted in the same area. The gas tank is fastened to that floatation

You can check that by measuring from the deck to the surface you want to mount the battery holders and then measure from the deck level to that distance on the outside of the transom to see if the bottom of the inside is the same as the bottom of the outside.

You shouldn't put the batteries on the actual bilge/keel/bottom where the bilge pump and drain hole is. The weight of them will crack the thin fiberglass when passing over wakes and waves.