I use Logbook Pro - I'm just about to upgrade to the PDA version as well.
I log each leg - it's a bit of a pain in the butt, but not much more than just logging the day. If you combine the flights do you do it by tail number (I might swap planes twice in a day, so now it's really not much better) or what? For me it was just easier to log it one per segment.
With APDL and the ability to load my pairings into it I'm ASSUMING that each segment will be pre-loaded and all I do is update the actual times, in which case it will all be even easier - but maybe not.
If I had any faith at all in the companies paperwork I might think about not really logging anything, keeping a copy of the company papers and just putting in monthly totals or something. But I find some many "errors" in the company times that it's just not going to be practical. And yes, I am interested in the day when they want me to fly something that's not legal but the company computer says it is - the planes FML will back me up - but maybe not before I've been fired - we'll see....
So that's just me.....