If the flash is the main light source marco, use external flash with a matching shoe cord.
The reason why people uses external flash is due to the length of the marco lens. The built in flash is not high enough. When you move very close to your subject, part of the flash light will be blocked by the long lens. A shadow will appear on your picture. I call this "lens shadow".
I always use a shoe cord, hold the flash and the lens with my left hand. both pointing towards the subject. This will shorten the distance between the flash and subject, and also avoid lens shadow.
Another reason is due to the higher power (also known as Guide Number) from external flash. For marco, you would want all or most of your subject to stay within the DOF. However, by increasing the DOF you have to reduce the aperture size. Thus, you'll loss half the range of your flash with every stop of aperture reduced. The formula for getting the effective range for your flash is
At ISO 100
Effective Range=(Guide no)/(Aperture Size)
At ISO 200
Effective Range=(Guide no)/(Aperture Size)*2
and so on for ISO 400(*4), ISO 800(*8)....
For example,
With f22, using the built in flash(GN 12m at ISO 100), your effective range is only 12m/22 = 0.545 meters at ISO 100.
For an external flash with GN 42m, the effective range is 42m/22 = 1.91m at ISO 100.
