What records should I make of underground infrastructure, before covering it up?
There are several things you can do:


Pictures, with clear reference points (eg, natural features of the land such as rock cuts, streams, as well as man-made structures). 
Drawings using graph paper, and with GPS marking locations
For non-metallic water pipes (anything without a metal wire in it), bury a metal wire alongside (really, any kind of continuous wire will do). This will allow you to use an inductive cable locater to trace that line later. There are also some newer RFID-based tags you can get that specifically indicate types of cable/pipe (power, water, waste, gas, telephone, etc), and can be read by a special receiver. 


Inductive cable locator: