The first page of my experimental organization typically displays the player with the most innings for each position. In this case, the Ace pitcher for the Twins in 1987 was HOF'er Bert Blyleven. Just in front of the pitcher is starting Catcher, Tim Laudner. To his right is First Baseman, Kent Hrbek. Above that is Second Baseman, Steve Lombardozzi. All the way to the Left is Shortstop, Greg Gagne. On the bottom left is Third Baseman, Gary Gaetti. On the top of the page are the three Outfielders, which from left to right are Danny Gladden, Kirby Puckett, and Tom Brunansky. The 9-pocket pages resemble a baseball diamond almost perfectly.
The next page features the manager and 8 other pitchers. I originally had the starting rotation in the first 5 slots with the manager in the center of the first page, but then switched the manager and pitching Ace. The second through fifth slots represent the second through fifth starters according to a combination of the their number of games started, innings pitched, and ERA. In this case, the starting rotation was filled out with Frank Viola, Les Straker, Mike Smithson, and Joe Niekro. The sixth slot is typically reserved for a pitcher that was involved in either a lot of games or innings with a relatively decent ERA. In this case, that pitcher was Juan Berenguer. The last three slots were reserved for late inning relievers in order by a combination of games finished and ERA. The last slot is what I consider the team's closer. In this case, the late inning relievers were George Frazier, Keith Atherton, and Jeff Reardon.
I'm not sure if this scheme of set organization will stick for me, but I'm sure that there'll have to be some slight adjustments to it if I do. I started doing this with my 2014 set, which doesn't have any manager cards, so I used either the DH, 4th Outfielder, back-up catcher, or some other player that was heavily involved with the team throughout the season. Of course, my primary resource for determining starting position players to organize my pages was baseball-reference, which is just so convenient. As for the rest of the team cards, I kept them in order my player age either just after, or just before the two full pages used to develop the scheme shown.