Well by using the plugin that rex provided here, i was able to "pause" the game and stop the sound/music whenever the popup was minimized. I just couldn't get it to start back up when the popup was reloaded :). I'm also still having issues with displaying the loading screen in pokki. I had a workaround where i display some custom HMTL text and images during the loading, but it increase the height of the popup(during the loading, but disappeared when the C2 game was fully loaded) which the pokki guys didn't approve of either.
Oh well, theres always next time :).