You can rename the save file to any other name you like. For example, if your last actual save is on page 110 in box 3, you could rename the developer save file "21-2-LT1" to "110-4-LT1" and then copy it to the save-file folder. This means that the save file will be on page 110 in box 4 on the left. In any case, I would only recommend using the official saves as a last resort. For example, if you deliberately ignore some story paths in your main walkthrough, but still want to know what happens in the game. In these cases, using official saves is a best choice.
In all other cases, it's preferable to have your own "full" save file (transferred from Ep1-->Ep2 v16--->Ep3) combined with a persistent file based on your progress through all 3 episodes. So in this particular case the best option is what is written in
FAQ 1.3.5 (under spoiler).