Depends on how you checked the projects out, if you checked them out as (literally “Check Out As…” from CVS menu) Web Module Projects you should be able to do the commands you want. You might have checked them out as Java Projects instead. Are you interacting with them from the MyEclipse perspective or Java Perspective?
This is exactly how I deal with my projects, so an FYI for you is that when you add struts cap, currently there is a bug that it will erase your ApplicationResources.properties file and I *believe* it may alter your web.xml file if the name of the action servlet doesn’t match the one you use in the checkout dialog.
ALSO note that your Web Context-root will incorrect be set to “/” after this checkout, you will need to fix that and change it back to your old app’s root “/myapp”. All these are known bugs (mostly because what you described is exactly how I work on all my projects) so I’ve run across them a few times.