I\'ve setup emacs 23.1.50.1 with CEDET 1.0 and ECB 2.40 (heavily inspired by Alex Otts setup at http://github.com/alexott/emacs-configs/blob/master/rc/emacs-rc-cedet.el and
When you get errors in your configuration, the best thing to do is:
M-x toggle-debug-on-error RET
and get the stack trace which will point at the problem area. Often times that is helpful in identifying the configuration issue.
CEDET will try to associate every file with a single project, and all the commands that operate in that buffer will be restricted to the bounds of that project. For the CScope support, it too will use EDE to identify the root directory, and that will help find the cscope.out file, and that is related to both the completion and reference tools.
The exception, of course, is the system include path which is usually /usr/include or whatever. This is an augmentation to the default system include path which is calculated with the GCC support. In one of your C files you can do:
M-x semantic-c-describe-environment RET
and that should show what Semantic will try to use.
To double check if CScope is being used for code completion, you can check with:
M-x semanticdb-find-test-translate-path RET
and check the end of the list for some CScope thing.