Hello Halcon,
I see this is a rather old request. I am just starting to do the very same thing. Did you ever figure out how to get the MicroC/OS-II running on a DE2 board? I have seen some instructions and an example in the textbook Chapter 18 (and 17) of "Rapid Prototyping of Digital Systems", Hamblen, Hall and Furman, Springer Science+Business Media, LLC, 2008 e-ISBN 978-0-387-72671-7. It is uses SOPC instead of Qsys, but I assume it would work with Qsys...
Would be interested in hearing about any issues that you encountered if you did get it to work.
Thanks for any info.