If it doesn't exist already, create a Gfx folder in the place where your save game data goes (My Documents\My Games\GC2TwilightArnor for example). Create Logo and Portraits folders inside that. Put the images in the right folders and you should be all set.
Images should be PNG format.
Portraits should be 256 by 256. For bonus points, if you can make a wide version of the portrait which is 430 by 280, you can use it as a static image to be displayed on the viewscreen when in communication with that race. This requires some manual editing of that race's raceconfigxml file to work, but it will eliminate that stretched-out look that custom portraits have by default in those situations.
