You'll essentially make a folder for first down WB, SG and PS defense, then a second folder for 2nd down WB, SG and PS and a third for third down defenses and so on as those settings are set per folder. The bad news is it's going to be a lot of work to start of with, the good news is once it's done you'll have one of the better defenses in the game. An alternative option is to put the defenses in the corresponding offense folders (ie your 2nd down defenses go in the same folder as your 2nd down offense) if your offensive plays correspond to your defenses.
As a side note, if you only put defenses plays in the folder the folder won't show when selecting plays.