With a false floor install, you'll lose your spare tire obviously. If you were installing a single sub, you often don't have to raise the floor at all because the tire well often has enough airspace for a single driver. Because you want to install two subs, you'll need to raise the floor for more airspace. This is actually quite easy.

Cut strips of MDF the width that you want to raise the floor height, and lay them along the edges of your trunk floor, standing on edge. Where they ultimately will need to be placed depends on the airspace you need, etc.
Use hot glue or whatever to adhere them in place; don't worry about strength on this part. Make sure all the edges meet along the same plane, because this is what the new floor will be mounting to. Don't worry if the strips aren't all the way to the edge of the trunk, it doesn't matter and they'll be completely hidden anyway. Now you're ready for the stinky stuff.

You have two options:

1) Make a permanent sub box, that can be removed in the future but it will be pretty damn difficult. If you want to do this, you can skip quite a bit of the fiberglass thickness and bond right to the metal. Get a drill and a sanding disc or Scotchbright disc, and remove the paint where you're going to glass. The advantage of this method is that you will use the nice rigid metal of the trunk as part of your box. Glass a few layers in the tirewell and up onto the MDF strips to tie everything together, and you're done with that part.

2) Make a removeable sub box, which will be heavier overall but easier to take out if you need to. If you're doing this, you'll need a lot more layers of fiberglass, and you should put down aluminum foil, masking tape, paking tape, whatever to make a release surface. I'm a personal fan of masking tape, it's easy to remove, and I brush a layer of silicone caulk over it to seal it and make it release really easily. I can't tell you how many layers of fibeglass to apply, it all depends on the contour of the trunk and things like that (contours are self-reinforcing, flat areas are not). Glass up onto the strips of MDF, and you have a one piece box. Now for the top.

A good rule of thumb is to use the stock carpet as a template. Just make sure your carpet fits the way you want it, and check it first. All you need is a jigsaw to cut out a big piece of MDF for the top of the box, and you'll probably have to trim a little here and there to make it fit the way you want. It might also be necessary to make the top of the box two pieces depending on the car. For this reason, make the top of the box before you start fiberglassing, so you can change things if need be.
I usually like to figure out where the subs are going to go, and then reinforce the top of the box with strips of MDF glued/screwed on edge under the top. A nice big X works great usually, and again, it's going to be hidden. Cut the holes for the subs, test fit everything, and once you're satisfied, reach through the sub holes with a pencil, and trace where the top meets the sides. Use this to locate the screws and predrill.
Screw the top down to the sides with the help of your favorite sealant/adhesive. Add some carpet, paint, vinyl, whatever you want, and you're done.

Oh yeah, don't forget to drill a hole somewhere to pass the wires through to the amp..

I can't count on both hands and feet how many of these boxes I've done; they're a pain but kick ass when they're done. Don't forget the polyfil..