I feel your pain! I have a self-contained class for middle schoolers with ED, but I did my student teaching doing Resource for K-4, so a lot of the same issues: weird scheduling, other teachers, etc. One of the things that really helped me for having lots of kids in different places doing different things was changing up the way I use the Scoreboard. I carry around one of those clipboards that opens up for papers. On the back every morning I tape a fresh 8.5x11 sheet of paper, and draw the scoreboard on it. Now the scoreboard travels with me instead of being in one location that I have to walk to to make marks. That helped immensely. I could also carry it to other rooms when I was doing inclusion and continue it.
We also had pretty small classes where the kids were all at different levels of low. Just because you can't mix them up doesn't mean they're not getting something out of working together! What I found helped was doing a lot of extra modeling at the beginning of an activity, since I couldn't depend on one of the students to teach the other.
Hope some of that helps! I'll post more as I think of it.
WBT Intern 2011-2012