Kenseido has it in the right. The Flaws and Extras simply apply to the individual powers in the array. There is an option broached in Ultimate Power of adding Extras and Flaws to Arrays where they directly apply to the working of the array (for example, using Unreliable so that arrays don't always switch when you want them to, or so that they only can be changed five times during an adventure), but frankly, it's more trouble than it's worth.
Regarding what Pergerine said, the original Core text did indeed indicate that you couldn't have a power at a rank greater than the base power. Ultimate Power got rid of that limitation (And the FAQ backs it up for Core
). Frankly, I think it should be a given since mechanically speaking, Blast 6 arrayed off of Leaping 12 is the same things as Leaping 12 arrayed off of Blast 6. Ultimate Power formalizes the process a bit by introducing a Capital-A Array, which is discussed in Delemental's post on arrays which you'll find at the link below. Oh, and you have multiple options when an array slot can't use all of its points. First, you can have multiple powers in an array slot. Secondly, you do have the option of not using all of the points.
By the by, I highly recommend reading through some of the items in Elric's thread
. In particular, there is an entry on Arrays that goes into great detail on how they work in various setups.