dknutson,
Managing libraries is more flexible and easy if you are doing it the MyEclipse way. Its easier to change the libraries version.
Also containers can be adjusted to the target server.E.g. if server has it’s own JPA implementation, you don’t provide additional JPA containers.
If you are using SCM and if you place your libraries under WEB-INF, then you need to check files in WEB-INF into your SCM (CVS, GIT) which means the libraries also have to be checked.
Hope this helps. Let us know if you have any questions.