manga with a villain as the main character? Like death note! Even though light was bad, ...

Code Geass sort of fits that description, but I am not sure if there is a manga, I have only seen the djs and the actual anime ...

So like an Antihero kind of character? Maybe try Berserk (though it's gory and explicit), Madness (it's yaoi though), Kuroshitsuji (i actually dropped reading this one but it fits the antihero thing) and thats all I can think of at the moment. Maybe look through the list at baka update:
https://www.mangaupdates.com/series.html?page=1&perpage=50&category=Antihero%2B%252F%2BHeroine%2509

Thank you! ^_^ I'll be sure to give them a try.

Try One Outs. Its a baseball manga with an evil protagonist.