I too have recently started adding more of my collection to the site. I'm hoping it will help me stay better organized. As I go through, I have a method that I stick to (team, then alphabetize the players). This is so that when I return the cards to boxes after adding them, they will be in some sort of organizational order. However, this is a very slow process. If I had to start over and didn't have a particular method, I would definitely add them on here by set. It would be so much easier to go through a set checklist and mark the cards that I do and don't have, rather than searching each individual player, marking a card or two, and then searching another one.
Of course, it is always to each their own. As long as you can find a method that works for you, you'll be just fine.
That probably wasn't a whole lot of help, but I'm still kind of new at this part too, so forgive me! Some of the longer-tenured members could probably give better pointers and ideas.
Jason
I'll never quit collecting entirely, but I am downsizing. Check out my COMC store and help me thin out what I don't want so I can buy cards that I do want. See something you like? Send me a message on here, and we can knock the price down quite a bit. I'll even take a bit of a loss if it means getting you a card you really want.