If you are referring to a general group of seven note scales, then you just have to figure out what notes are used in which scales and apply them to the song. If you have the notes you want, you can then come up with a chord. Most people do it in reverse though, if you want the key of the song in A, then you should automatically know which notes are used in an A chord and determine which mode they would use as far as the "root" note is concerned. Those notes are then generally used to determine a scale. I know you probably know this already, but it basically helped my to determine which progressions to use in song writing. Gotta use your ear. Hope it helps...

Also, to add to what you asked before...If you know your modes in order, then you just need to develop a key signature for the song. Chord progressions come from key signatures or assigning a root note. If you choose say "Aeolian Mode" in the Key of E, then you can use the mode to determine which chords you can use by what notes the mode uses. (GMaj, Em, CMaj, etc).

Try this quick lesson to see what I mean...

http://www.theorylessons.com/usingmodes.html