I have the same bottom-up setup you are building, tlc, though it's an Aquascape Biofall instead of a nice big hole in the ground. My filter box drains onto a slab of flagstone about two and half feet above the pond. Pump is rated for 3000 gph, but my guess is that it's moving a little less than that. Some of the falling water hits rocks there, and some hits the surface of the pond. It makes a really wonderful sound.
I have a green, medium density matala pad, then two blue, high density pads, then bioballs. Why these materials? Because the pond came with them. Though bioballs don't clog up easily like lava rock, the reason for this arrangement is that the balls are rather difficult to clean.
Will you have any mechanical filtration before the biofilter? I highly recommend it. The downside to a bottom up filter is that you have to take everything out to clean it. Some claim that with a big enough biofilter you don't need to do this, and I suppose with a very large filter and a very small load that's true. But I've read posts by a number of folks who tried to go the "Skippy" route and discovered that pond debris does not in fact turn magically to sand. If you think about it, all that stuff is still in your water, and unless you have very few fish and no trees, it's probably not a good idea to leave it there.
Since I installed a skimmer with a filter, cleaning the biofilter has been a lot less work. The new skimmer came with a very dense filter pad, almost like something you'd find in an aquarium filter. This needs weekly cleaning during some parts of the year because it tends to clog up with pine needles, but easy and it's worth it because it keeps most of that out of my biofilter. Very little debris reaches the biofilter now, and the green pad caches most of it. If I were building this type of system from scratch, I'd have a skimmer basket, then a series of pads or screens, strictly for mechanical filtration, then the pump, and finally a big hole full of pot scrubbers. Pot scrubbers have about three times the surface area to volume as bioballs, and are
much cheaper.
I don't have enough bioballs to fill my filter, so I'm going to get scrubbers. Because the scrubbers are so cheap and provide more surface area, I'll probably take the bioballs I have out. Maybe I can find somewhere to hide them under the waterfall or float a few in the skimmer.
You might want to consider a horizontal filter. Here's a good article on that and other things:
http://www.akca.org/library/filter2.htmAnd if you run across them yet, wet/dry or trickle filters have extremely good performance because they provide more oxygen for both bacteria and fish. This type of filter will freeze if you don't shut it down when the weather turns cold, though.