Well, first things first, this project is not for a "Hack ROM" game, you need to use RPG Maker XP.
To use the Gen Vi project you need to make several chances in the Script Section (Programmig part) to add moves effects, abilities, and other things.
The same goes for Mega Evolution, which can be done at Script Sections, the current version of essentials have some few examples of Mega Evolutions in the MultipleForms section.
Also, you need to make changes in the PBS files, where the Pokémons species, moves, TMs are stored (this can be done in Notepad and does not require any scripting knowledge).
And you also need to get some new graphics for the new species and Mega Forms. Just put them into "Battler" folder and name them the number of the species in Pokédex, as for Mega Evolution add "_1" after the Mega Sprite name. Like Venusaur is "003", the sprite of his mega evolution should be "003_1".
Remeber that this is not a full tutorial, just a little help for understanding how to make the changes. I may have made a mistake at some point, but check the thread of the "Gen 6 Project".