What's the best way to take care of the rust
> above the rear wheel wells that allows water into the trunk? Looks
> like a mess.

Get a spray can of rubber-based, self-curing black insulation. I
think 3M makes something like this but I haven't seen it in years
(haven't needed it again). It's a black, spray-on slightly foamy,
slightly expanding sticky stuff that hardens in a few minutes to a
solid and non-sticky rubber material. Automobile paint store or some
specialty shop should have it. Also you need some "tin snips" and a
piece of thin sheet steel.

You snip a piece of steel to fit over the hole, then spray the rubber
around the edge of the hole, and place the sheet metal (it should
stick, even horizontally, or hold for a few moments if necessary).
Then spray the upper (if visible) and lower piece of sheet metal all
over, let it all dry as you move to the next hole. End product is
absolutely professional looking, keeps the water out, you'd never know
it had rusted thru. Total cost maybe $30, less if you already have
the snips. I did this many years ago. It was a simple fix, worked
great for the life of the car, actually fun, and protected from
further rust.