Some seaplane bases have prescribed areas for landing, but are the landing areas marked by buoys or lights? If so are "runways" outlined in the water or just a general area?
Do they have IFR approach procedures?
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Are the landing areas marked by buoys or lights?
In at least one specific instance, Yes.
The seaplanes that operate out of Lake Union, Seattle, have "Advisory Buoys" that help make the many sailboats, kayaks, and motorboats on the lake aware that planes will be arriving or taking off.
The buoys have Pilot Controlled Lighting (PCL) that will turn on yellow flashing lights. They are typically activated approximately 3 minutes before any departure or arrival.
The buoys do not restrict boat movement; they are advisory only.
The busiest water aerodrome that I know of is Vancouver Harbour (CYHC) in British Columbia, Canada, which has over 50,000 movements a year, as a hub for a large network of seaplane commuter routes up the coast and across to Vancouver Island and down to Washington State. Busy enough that it's also the only water aerodrome that I know of that has a positive control zone with a control tower (at the top of a harbourfront office building).
There is no instrument approach however, and airplanes land in a general area in front of downtown as necessary for winds and to avoid boats, riptides, deadheads, and the wakes of ships. All the flying in and out is VFR, although often in conditions you would think of as IFR.