Firstly congrats!! I have a few completed sets but none of them mean much to me. not like yours. (They came to me that way. No fun.)
I have all my cards organized in the only way I see to be right for myself, by year, by set, by number. The reason? I can find any card in my collection in under 5 minutes and show it to you if you want. I know where each card is within approximation. To each their own, i used to do the teams and then I did the players all separate, still by year and by set and at times by numbers. I just don't have the time to go through and change the organization of 12,000 again, and this works!
The difference between Hoarding and Collecting is Structure.
~Kris~