The side with the USB pins is the top side. The link cable has to be plugged in with the rounded edges of the plug to the bottom.
The USB-MIDI adaptor has three different MIDI modes for use with any MIDI-enabled PC-program. To set it to a specific mode, use the utility (download: Win / Mac version) with the following commands:
By default, the adaptor forwards MIDI signals from the USB port to the Game Boy's link port so that it can be used with mGB out of the box, without using the utility. On the PC, you just have to select "nanoloop MIDI" as output port. It is recommended to deactivate sync.
Sets the adaptor to nanoloop / LSDj sync mode. Once in sync mode, it will only listen to clock/start/stop messages and send the appropriate signals to the Game Boy, so that nanoloop / LSDj run in sync with a PC program. In the program, select "nanoloop MIDI" as the MIDI port for sync output.
This command inverts the direction so that MIDI signals are sent from the Game Boy to the PC.
The adaptor performs no parsing, each byte is forwarded as it is, may it be valid MIDI data or not. Using this function with random non-MIDI data from a Game Boy program may confuse/crash a PC software and / or the USB / MIDI driver.
When using the above commands in capital letters ("-SYNC"), the mode will remain set when the adaptor is unplugged.