Copying the .cod files into the simulator’s directory (where all the other .cod files are) and restarting the simulator will work.
Probably though you want to automatically deploy from Eclipse. If this isn’t working for you, there are a couple of things to check:
Check that the project has been activated for BlackBerry – from the right-click menu for the project, make sure that Activate For BlackBerry is checked.
If that’s already checked (as it is by default when you create a new BB project), then sometimes explicitly building the project will do the trick: From the Project menu, choose Build Active BlackBerry Simulation
EDIT: In response to some comments below I thought of something else. The configuration you choose may have something to do with your problems (BlackBerry -> Build Configurations). The configuration in the JDE Plug-in doesn’t affect the code generated, but it does affect which projects are activated for BlackBerry. If you switch configurations, your project may become un-activated.
Since it doesn’t affect the code, I usually just pick one configuration and stick with it throughout debugging and release.