Was Bill evil for the sake of being evil or did he feel he was doing the right thing?

Interesting question. Given the long speech about comics at the end, I believe he was evil for the sake of being evil. He wanted to be the comic book villain. And creating the Deadly Viper Assassination Squad he created the anti-X-Men. Although his speech was about Superman I don't think he minded between DC and Marvel, just to be the best of Lex Luthor, Dr. Doom, or any other evil comic mastermind.

I think he probably saw himself as being a bit of a superman - in the Nietzsche sense, not the comic book sense. Maybe that's why he liked the comic book guy... Or, if you prefer, he is a "successful" Roskalnikov from Crime and Punishment. He imagines himself as being better than everybody else, above such petty concerns like "morality" at all. In other words, I don't think he thought of himself as evil, but rather that he just ignored the whole "morality" question. I think that's what makes him such a scary and horrible villain, too. That's why Hattori Hanzo is willing to break his oath to God to never make another weapon: it's to go after the Devil.