First, download a clean PKMN ROM. By "clean", it means that it's not hacked. The PKMN ROM you will download should match the ROM base of the hack you wanna play.
Then, download the patch of the hack you want to play.
Then, download the patcher that suits the patch.
Patch the patch to the clean ROM.
Open it with Visual Boy Advance and presto!
So, since you wanna play Flora Sky, you need to download the patch of it, and then a clean Emerald ROM, and the UPS patcher.