If you're using Nintendont, you don't need USB Loader. For Nintendont, your USB/SD card's contents should appear as follows:
(Root of USB/SD)
games
---E01
game.iso
---E01
game.iso
In which "---E01" is the game ID you've assigned to 3.02 and 4.0 Beta04. By default, Melee's game ID is GALE01. You can't have ISOs with identical game IDs, but ISOs will still be recognized as Melee so long as the last three characters "E01" are present.
Google for HxD Editor and download it. If you open the ISO file in that program, you'll be able to change the first three characters of the game ID (near the top) to anything you want. You'll receive a warning if you perform any actions that will change the total number of number/letter/symbol characters used in that...coding file text thing, so don't hit backspace or delete. (Typing anything will just replace the next character, kinda like on a graphing calculator.) G02E01 is a commonly used game ID for 3.02. If you want to change the game ID for 4.0 Beta04, I would suggest something along the lines of B04E01, so you can keep track of the beta version/update.
While still in the HxD Editor, you can also change the title of the game as it appears on the Nintendont screen so you don't get confused later. For example, "Super Smash Bros Melee" can be changed to say "20XX 3.02" or "20XX 4.0 Beta04". Make sure to fill in blank character spaces with periods "." and not spaces " ".
Edit: Sorry for sending you over to the 20XX thread when I could actually answer your question lol, I just misread it the first time and wasn't sure. If you haven't posted there already, feel free to just ask further questions here. You should check there first on future occasions though.