Just do both... but the anime would be easier to follow because scans of Pokemon Special (it's known as Pokemon Adventures in the US) are very hard to find, and English volumes expensive to buy relative to the anime, which can be viewed for free if you live in the US and have either cable/satellite TV or an internet connection. The anime is also easier to find online, both for questionably legal sources and perfectly legal sources, at least in the US, as the official US site (Pokemon.com) has currently has 24 episodes from the Johto arc up online.
I find the story more interesting in the PokeSpecial, though, but that's just me. It's got much more continuity and has a darker story than the anime (though that's not all that hard to accomplish).