Hi Gringo6...

Just read your post and here are a couple of Links you might find interesting.

http://avstop.com/seaplane/50/ch8.html

http://www.flightsim.com/main/howto/ndb.htm

http://www.pilotfriend.com/training/flight_training/nav/adf.htm

http://en.wikipedia.org/wiki/Instrument_landing_system

http://www.navfltsm.addr.com/vor-nav.htm

There are also various rules and regulations governing civilian aircraft/helicopters when landing and during take-offs and in Canada these one can access through the internet by typing in Transport Canada.

The military in most countries operate within the bounds of that countries civilian rules and regulations however they do have terms like "Operational Commitment" etc. etc.

Now years before the VOR was invented we would tune in radio stations and NDBs and get a fix.  Still can.
We could then do an approach off that fix. Timing and nerves of steel was everything...

Now this worked great flying your PBY5A onto paved runways or frozen large bodies of water in less than ideal flying conditions, however landing on normal water was a little different.  It was usually a powered on approach all the way. 
There are also landing and take-off rules and regulations governing hours of operation off water for civilian float aircraft and again these can be obtained through the Transport Canada Web Site.
An endorsement to the Pilots Licence is also required.
This endorsement is quite expensive but includes Ground School, Dual Flying Time and Solo Flying Time.  Yes there is an exam as well.   Well worth the cost as float flying or seaplane flying will open a whole new realm of flying.

Doing an instrument approach into a land based airport with an amphibian was no different than any other aircraft.  Where the difference is when landing on water at a non Water Aerodrome like a bush camp/fishing camp.

Now I know there was some military testing with fixed underwater landing lights during and after the Second World War but never seen any results from that testing.  I would imagine that was at secret military bases far from the publics eye.

Lighted Floating Buoys are used at Water Aerodromes in Canada.  Many locations you can see lighted markers on the shore which will border the landing path.
There is a Transport Canada Water Aerodrome Supplement published once a year and unfortunately you have to purchase that like all the other publications.  A must for anyone operating off water and an excellent source of information. 
This publication gives all the information about each Water Aerodrome in Canada.  Fuel, Oil, Nav Aids, Lighting, Accommodations, etc. etc.

There is also joint testing between the militry and civilians on  better instrument landing systems and collision avoidance systems.

I do know a couple fellas that flew the Sunderlands in the Royal Canadian Air Force and I shall ask them about the different techniques they used as I only flew the PBY5As/Canso with dual ADFs.  They did update them with dual ADFs, dual VORs, GPS etc. but I was then flying something different.

Not sure I was much help but if I find anything will pass it along.   

Cheers...Happy Landings...Doug