1) In MMW, if the device isn't connected under Tools > Options > Portable Device Sync.

2) If you use Auto-Conversion on Sync (recommended) you'd have MP3's on your device and FLAC on your PC after Sync. If you use Tools > Convert Format in MMW it depends if you enable replacing or not.

1) I can't seem to find Device Profile, is this in MM4 on the PC or phone?

2) If I use Tools > Convert will I end up with two files of each song in the directory, the orginal flac and new converted mp3?

You can do this during Sync by setting Auto-Conversion in the Device Profile (which leaves originals on PC in the higher quality FLAC). Otherwise just use Tools > Convert Format on selected files.

Does MMW have an option to convert a flac file to mp3, singular or in bulk?

I have a couple media plays that seem to have slight probs when playing flac files. They play the files just fine but the pause momentarily randomly, usually only once per track. I figure the player is choking on the large flac files. I never have any issues playing mp3s.