What do you mean custom? you can add whatever you want to a supply drop as long it is an ammo crate or a vehicle.

When I say "custom" I want to select the item in the supply crate and how many of each item there is. Will I have to drop a bunch of different crates to get the total amount of items I need, or is there a way to create a custom crate in the editor or MCC?

If you edit any vehicle or crate with Zeus while using MCC you'll have an option to set the cargo's items of that object.