it is simple... it is like having 2 graphics cards...
workbench uses the RTG card (in this case the vga on the mediator) as some games that have rtg option.
but if you plan to play whdload games, that "talk" to the amiga hardware directly, they will use AGA only, and there is no way to change that. so, you have your monitor plugged on the pci card, and you start a game that uses AGA, so u need to plug the monitor to the aga output, a scandoubler in this case, to see the game. so if you have a switch you press a button and it switches. if you have a dual input monitor you press it's button, and if you have a zorro based rtg that has a built-in automatic switch (like the picassoII, piccoloSD64) it makes the switch auto.
I hope you get the meaning of all these... :-)