The anime series doesn't end conclusively:
With Mystletainn's defeat Merry's past is still unknown and "Pharos" Hercules's plans is still in motion being unaffected by Mystletainn's death.
So I am wondering, how much of the manga was adapted into the anime? And are there any deviations?
In this case, the manga and anime really weren't very close at all. The most reasonable place to say that the anime ended is at the end of chapter 12 (i.e. the end of volume 2). The manga volume 2 ends with Yumeji learning about Engi and Yui. Almost everything after that in the anime is original. Even before that, there are several very significant changes, so I recommend rather than starting at volume 3, read from the beginning if you want to read the manga, or else you'll probably end up confused.
