In the special features section of the Sword of Stones DVD, there is a panel discussion featuring Mike Mignola, Guillermo Del Toro, Tad Stone, and others involved in the Hellboy Animated projects. Tad Stone is the driving force behind the project.
The panel has Mike Mignola talking about why each of the three mediums (comic, live action, and animated) have differing story lines and looks. For example the live action movies have Liz and Hellboy in love while nowhere in the comic is that a feature.
Mignola says in the discussion that he wants each of the ventures to be different. He wants all of them to feel like a Hellboy story but the mythologies and facts do not have to coincide with each other. A good example of this is that in the comics and live action movies Professor Bloom is dead while in the animated projects he is still alive.
This is something to keep in mind if you plan on watching the series. Its still Hellboy but its not following or continuing from any other medium, it is its own animal.