Easy Blogging and wpmu-nelo functions?


I am wondering if the easy blogging and wpmu-nelo theme are 100% compatible together?, and if i add in the menu section of easy blogging the "themes.php?page=functions.php" where users can change colors of wpmu-nelo and those options that are available for that theme is that working in Easy Blogging mode?. because it does not work here. I have also tried using the Easy Blogging mode on few themes that have some color options and things like that and that never works.

Just wondering if some other people are also phasing the same problem with easy blogging and custom there options/functions?