The following explanation is provided by me, compliments of our good theory friends over at Harmony Central.
Confusion over minor keys is often related to the fact that the natural minor scale (aeolian mode) does not include a major V chord. In C (natural) minor (C D Eb F G Ab Bb) the diatonic V chord is a G min (G Bb D).
The problem here is that we really want to hear the leading tone to tonic resolution/movement, both melodically and harmonically, that requires a major V chord G (maj) (G B D) to the I minor chord C minor (C Eb G).
This "problem" is what leads people to modify the natural minor scale by playing around with raising the 7th and or 6th degrees from Bb to B natural and Ab to A natural, respectively.
The chords of Cm and Fm are both in the C (natural) minor scale (aeolian) but the G7 chord is not. (It is available from the Melodic minor (C D Eb F G A B C) and Composite minor scales (C D Eb F G Ab A Bb B C)).
As long as you keep to chord tones and low level extensions you'll be able to use C natural minor over the whole song, but just stay cognizant of the effect of playing a Bb (effectively a #9) over the G7 chord (G B D F). For this one chord you're probably better off avoiding the Bb and instead use the B natural and the other G7 chord tones for a more "inside" sound.
The minor keys are always harder to explain than their complexity deserves. For simple stuff you can normally just think in terms of the natural minor and modify that scale to include the chord tones for whatever chord is not diatonic. The central sound most often returns to the natural minor scale/key. In all cases you can just add up the notes in the various chords and use those notes to assemble an appropriate scale, but this too leads to confusion regarding available tensions and passing tones. The problem comes in when people expect all the notes in any one scale to work over every chord. That is why some of us prefer to think in terms of chords and chord scales with available tensions rather than in terms of one scale for all of the chords in a song.