Sadly, the technologies are different between the two and you can't combine them.
On the regular +12V RGB header (4-pin), all LEDs of a primary color (R, G, B) are chained together and act simultaneously depending on the input signal. This makes individual LED addressing impossible.
Pinout:
pin #1 - +12V
pin #2 - G (green color)
pin #3 - R (red color)
pin #4 - B (blue color)
On the +5V RGB header (3-pin), there is LED driver IC for each RGB LED package that translates the serial information coming in through the data pin into a specific output for that LED package it is attached to. That method makes single LED addressing possible.
Pinout:
pin #1 - +5V
pin #2 - data
pin #3 - empty (no pin)
pin #4 - ground
Plugging the 3-pin RGB...