you have to set up a coverflow for your emuflow. those are not set in the ini of the theme. just go to the settings when your on the coverflow for your emu, an set it up an save it.My second problem is that whenever I add a theme, I don't get all of the Bells and Whistles when I view my covers on my EMUFLOW( 1 and 2 buttons do nothing). With my Wii and Gamecube games, I can press 1 and 2 and am able to switch views regardless of which theme I set.
( this is what i do to get a different view of the covers on any given coverflow.( emu, plugins.ect.). if you want to add, the coverflow to a theme that doesn't have your custom flow.
open note pad ++ copy/paste the coverflow you want from the default ini to the custom theme ini, adding the correct number to the line. for instance, emunand coverflow1,emunand coverflow2, ect..( the more coverflow's is were 1/2 come into play.), but be careful the more coverflows there are, the more likely you'll get a stack dump error.(just one of those things..) i have three sets of coverflows for each view, an have yet to have a stack dump. haven't tried more.
as far as the first question, i don't use the "source menu". i just use i guess the default (were you check the plug in.).. cause the only plug in i use is mplayer. so no need for the other crap.