I am still a relative newbie to Media Center, but I believe that the thing to do is to keep all of your media in a single library at the highest quality format available. MC will then transcode on-the-fly to whatever format a particular device can handle.
In my case most of my music is MP3 because when I captured it back in the day it was intended for an iPod. But all of the newer music that I have ripped since becoming an MC user is stored in lossless APE format. I use JRiver's Gizmo app on my Android phone for remote listening; MC transcodes my APE files to MP3 when streaming them to the phone. Similarly, when I export files to iTunes on my wife's laptop, MC transcodes them to MP3.
So my advice is keep all your files in a single library, in FLAC format where you have it and in MP3 format where you don't. Then export or stream to whatever environment you want and Media Center will take care of the format.
More experienced MC users can no doubt correct any mistakes on my part and advise you of the details of how to set things up.