Lava rock will work (at least in KOI ponds) but it is a lot easier to clean if you have it in a consolidated location. Bigger fish make bigger solid wastes which will clog Biofilters, so cleaning is something you want to consider.
Everything that the water touches could develop microbes, but you will need alot of surface area to convert the bioload produced. It would be a good idea to figure out what your Bio-load will be and then figure out how much lava rock you will need to meet that load.
There are some people who really hate underground filters and they list some compelling reasons why you should stay away from them. try googling ugf filters and I am sure you will find some good info.
