I have a large (actually 2) 3-ring binders that contain every bill and
work order that I could find. They're organized into Avionics,
Engine, Structure, ADs, SBs. Every oil sample test (and bill) is
in the Engine section. All the annual inspections are in their
own section. Does this mean cross-reference? Possibly, but I'm
focusing on the billing. I've been scanning the log books (slowly)
and as one book is finished, it goes to the safe deposit box along with
one copy of the logbook on CD. The other copy of the CD is at home
in one of the 3-ring binders. I also got the FAA records on CD,
made a copy of that, also in the safe deposit book. Since the
work orders all have the date on them, it's easy to match to the
logbook entry.

You'll end up organizing in way that makes sense and is practical for
you, since it's your aircraft. Have fun! It's the perfect activity for
one of those rotten thunderstorm days when you can't go fly.