Bootable USB drive, but with files in sub folder?

I created a bootable USB drive which works as expected, but it creates a bunch of obscure files cluttering up the main storage space of the flash drive. Will it still work if I put these boot-files in a sub folder?

Also, is there a way to put multiple bootable images on 1 flash drive but be able to select which one when in the BIOS? For example, if I wanted to create a flash drive bootable version of Ubuntu and Acronis Rescue Media, 1 one physical flash drive, would this be possible?

You cannot move the obscure files to another location as the bootloader and subsequent programs that execute will look for it in the location they currently are in.

As for multi-boot take a look at YUMI – Multiboot USB Creator (Windows)