Middle school was hard for my 'quirky' girls (no diagnoses, but they have always had a bit of a hard time fitting in, few friends most years, academically very high, etc) but they each were able to find a small peer group that accepted them.
One daughter found her niche in a group of kids that would most likely have scared the pants off of me when I was in school, but they kept each other safe, accepted her for who she was, and never caused any serious trouble. She knew what not to do, even if they were doing it, but I kept tabs on her at all times. She has since moved on from that group, and connected with others. She even has a boyfriend! (Yes, I'm watching that scenario very closely too!)
Second daughter was blessed to find a cluster of other 'quirky' girls (I'd direct you all to their
YouTube video, but I want them to remain anonymous here) that really boostered her self confidence in middle school. Too many of them went on to other schools this year though, and we had a rough time at the beginning of school. She's holding her own, but I wish she had her full support group still intact.
For middle school, it's very important to find the person who has the most influence over peer group behavior, scheduling, etc. and make that person your best friend. Sometimes it's the guidance councilor, or the special education co-ordinator. Most times it's one of the aides, who gets to witness things as an almost 'invisible being' to most kids. That person can suggest peer groups for your child, or how a schedule could be altered/tweaked to give your child more support. Of course the aide can't do the actual changes, but he/she can give you some great hints and info!