What do you do when your ociation with a problematic employee causes your employer to see you in bad light?

I started the same day as this other employee, so naturally we turned to each other since we were both new and didn't know people. Now, after a year of going to lunch everyday our employers think we are one. Although we have different work ethics and morals and she's a drama queen. So because I'm more quiet they just call me by her name also since we're lumped into one. So, we've had these two very rude miserable coworkers that bully around the whole group, particularly picking on us. But, the employee i'm lumped in with wrote a note to human recourses stating how they are, and now I'm lumped in with that note and feel tainted. The management doesn't see how much the workplace bullying is going on, so figure we're the one's attacking the bully's. Any advise would help...I know I should stay away from the drama queen now, but any other advise on how to tell my bosses I'm not ganging up on the people bullying others?