WBT works with ANY class size! I student-taught in a remedial class like the one you've mentioned, and I wish I had had WBT (it was 7th Grade Lang Arts) It is absolutely great in Middle School. Most of the students probably think you are a "dork" anyways, and it is SO much fun to get them involved. I present it as a kind of "Ok, I know I'm dorky, but I'm letting you play games and get out of your seats... have you been allowed to move this much and make this much noise in other classes?"
As far as the PowerPix go, look over the PowerPix since many of the concepts pictured may still work in your classroom. I teach 5th and 6th grade and I know even though the standard/PO numbers are different, the concept is similar, ESPECIALLY since the kiddos you teach are a few grade levels behind. One thing you might try is to download the Power Pix and, depending on your tech-savvyness, either print and white-out or photoshop out the standards. My experience is that the kids KNOW they are in a remedial class and do NOT want to be reminded of the fact that they are learning lower stuff.
Speaking of which, one of the best things about WBT is that it is SO customizable. One of the mantras is Keep a Big Back Pocket and It's a Long Year, so you have PLENTY of time to implement what works for you and your classes. My years in sixth grade worked like middle school, I only taught Language Arts and the kids rotated to the rest of my team members for the other subjects. This meant I kept four charts on the wall with four different goals... It seems like a lot of work, but I had four "sections" on most of my bulletin boards for each "group" or period, so I just moved to the next chart when the next set of kids came in. (I had previously tried to keep track of it the other way, using one chart, but we were using longer term goals that would span days or weeks at a time and the kids didn't want the other classes interfering with their points, so it was easier to keep four different charts that I just covered with an overhead sheet and used dry erase on.)
As far as the WBT for Challenging Kids and Power Teaching for Challenging Teens, I know the program USED to be called Power Teaching, but maybe a guru with more experience than me could clarify?