Mega Evolution Table Structure

The GARC for Mega Forms is a/1/9/3.
After unpacking, there should be files 000.bin-825.bin
Each Pokemon corresponds to their PokeDex Number.
Charizard is 006.bin, for example.
Without modification, each file can contain three Mega Forms.

Open up the file, for the pokemon you want to have a mega, in any hex editor.

The first two bytes are the form number, where 00 00 is no form and 01 00 is form 1 etc. (00 00 = no mega)
Deoxys, for example:
00 00 = Normal Form
01 00 = Attack Form
02 00 = Defense Form
03 00 = Speed Form

The Next two bytes determine the type of mega evolution. (Rayquaza)
01 00 = Item Held
02 00 = Dragon Ascent (I think, haven't tested)

After that there's two bytes that determine the item:
I used  http://pastebin.com/NnuPxfNh (by Kaphotics) to figure the Item IDs, on the left side of each item there's a number, you need to convert that number to hex.
100 = 64
Next you need to place it on a 2 byte array:
00 64
Then you just swap the order:
64 00

The last two bytes are 00 00

After that there should still be 16 bytes (0x10) left for two more megas.

proof: https://www.youtube.com/watch?v=2jcx86k-yvE