When the device boots, it searches SD:, USB0: and USB1: in that order, for supported disk images. It will recursively enter directories as it encounters them, so it may search a subdirectory on a disk before finding a file (e.g. it may find usb0:/a/game.iso before it finds usb0:/game.iso). This is dependent on the order in which files are stored in the filesystem on disk.
ISO files are supported. By default, the firmware will assume a normal sector size of 2048 in mode1 (as per a normal CD or DVD), but it will inspect the contents for an ISO9660 header to detect certain other sector sizes (e.g. CD-i formats, used by at least one Namco246 game).
To support other formats explicitly, alongside audio tracks, the game will also look for CUE files. Regardless of whether they're a single BIN file, or split into BIN/WAV, the firmware will attempt to parse the CUE correctly and load all relevant files automatically. This provides support for various CD-i/Mode2/etc. formats.
Some basic testing has so far revealed the following statistics. Updated firmware in the future may change these rankings.
USB0 is the fastest port, running at USB high speed (480Mbps). Via a USB OTG cable, you can connect a USB Flash drive and store your disk images there for maximum possible access speed. Thus, this is the recommended solution.
SD is the second fastest port. Almost as fast as USB0, but the port can be a little tricky to insert.
USB1 is the slowest port, running at USB full speed (12Mbps). Though it will support a disk if it's connected, this configuration isn't recommended, though is fine for firmware upgrades, connecting to a computer for command line access, and general I/O (e.g. ethernet, external control pads, and other future features)