Clay,
1) Yes, you can have as many struts-config files as you like, but for the editors creation wizards to work properly they need to be contained in a MyEclipse web project to which you’ve added struts capabilities.
2) You may not be missing anything. The flow view is still “a work in progress” in the 2.7 RC2 release. In fact, a completely new version will be introduced in the 2.7 GA release and that should address any shortcomings of the current one.