You probably heard about home brew because sky is advertising as they support it, and that's why you're thinking those files should be fed into flashcard. The fact is that sky has nothing to do with hb. Hb supports all legit game cards, and sky can be supported only because it simulates real cards. Since you're new to this I'll make this clear: copy everything from starter kit to the root of 3DS's sd and keep all the other on your sky. Then you shall be fine.Interesting - I did not read about this.
I will give this a try now and report back.