I'm not a running expert, but I believe it is best to alternate during the run. The technical term for this is 'Fartlek' (pronounced 'fart lick'...honest, I'm not making this up).
You can read more about it here:
http://en.wikipedia.org/wiki/Fartlek
I've tried the training and it really does help with your stamina, quickness, and, most important, your recovery time between points.