My plan for that is using plexi glass and attaching it to the bottom and sides, drain in the middle to a canister filter and back out the back into a waterfall over stones back to the pool. Line the pool with some small slate to hide the plexiglass. Depending on the size of viv you are putting together this may or may not be an option. You can always make your own pond with a plastic tupperware container or something, you could use mosses/stone to hide the edges, or use a black silicone. Be creative
If you can have your tank drilled that is the best way to do the plumbing for it. Also having a drain below the substrate (do a false bottom) will help you avoid excess water down there which can cause problems.
In my test viv I used a 4" PVC sitting on the bottom with holes drilled and it runs to the top of the substrate so I can syphon excess water out that way (hidden by a fern). You can use a cap/screen over it to keep the critters out.
For my fire belly toads I used shultz aquatic plant soil on the land side covered thinly with sphagnum moss, then live backyard moss on top of that. The water section just has inert aquarium gravel. The toads have never tried to eat anything but bugs, my finger, each other, and the ocasional guppy fry. http://photobucket.com/albums/a257/y...%20Paludarium/
There are some pics here if you want to see what I'm talking about.