Power Jack goes to the DE10 Nano.
Supplied SD card goes in the DE10 Nano.
Supplied USB cable goes between the Jamma card and the DE10 Nano.
Rgb switches Jamma , vga - Based on the Silkscreen I would say ON is for Jamma Video and OFF is for VGA connection
Kick 4,5,6 switches ? ^ small jvs button & switch ? - These switches I believe configure if buttons 4,5,6 are connected to the Jamma connector or the Kick Harness,
thats not a JVS button, not sure of its function but the JVS silkscreen is referring to the USB connector which is JVS, Switch is for switching the controls for Player 1 and Player 2
OVR/AUTO switch I believe is for video settings, see Mister CRT information linked above by another forum member, it references this switch in the settings.
Power Jumper is for the User Port, if your not using the DB15 SNAC Jamma edge adapter then leave it as is.
There is a but of information on the Acade Projects forum
here, but it appears the board has been revised since the original information.
Weirdly mine is a different variant from yours, Rev E, although checking a 2nd one that just arrived it is the same Rev F.