you might want to try this method,
Create a playlist for your iPhone and/or iPod.
Move all the tracks that you want to be on those devices, into the playlist. Make sure the check marks are in.
Connect the device and under the music tab, choose the "Selected playlists, artists, albums, and genres" option"
Put a check mark in the box next to your newly created playlist in the Playlist window and you will be good to go.
At the next sync, only those tracks that are in the playlist will go to the iDevice, complete with checkmarks, leaving you to play tracks from your library without bothering to add/remove the checkmarks.