I'd suggest just keeping CFI signatures in a paper log book. Current FAR's require written logbook endorsments (even on a McDonalds napkin is ok) but there is no provision for 'electronic' signatures in the FAR's. I still keep the name of the instructor (or student) in the remarks section in LogbookPro, but definatly keep all endorsements and such in a paper log. (This is from an AOPA interpretation that came up from a question at a recent flight instructor refresher course I attended.
For what it's worth,
Larry