I\'m working on an MFC application, that got pretty messy over years and over different teams of developers. The resource.h file, which contains all command/message mappings
Generally, there is no need to insert or edit the identifiers in resources manually (identifiers assingned by VS automatically in a correct manner). There are some cases that require manual interference in identifiers, but you can start with assumption, that work of previous teams of developers with resources was right. So if you did not encountered a problem because of resources, keep them untouched (IMHO).
"MSDN docs mention that Command IDs and Message IDs should not be less than WM_USER and WM_APP correspondingly." - It seems you something mixed up.