The facility to make a package and then move that package to another server is very good. However, if you package a site that uses a custom template, the package does not contain the files needed for the custom template (because they are stored in the Autodesk Infrastructure Web Server Extension 2014/www/fusion/templates/mapguide folder, not in the Autodesk Infrastructure Map Server 2014/Repositories/Library folder). This means that you have to remeber to transfer the template folders to the new server as well as the package.
Is it possible to have custom templates included in the package?
This isn't really possible because you're trying to bundle things that reside in 2 separate tiers
* Your data (server tier)
* Your application code (web tier)
The packaging functionality only concerns the server tier.
However if what you're after is a package that has everything included, you can zip/tarball up your custom template code and (ab)use the resource data mechanism to attach this zip/tarball as resource data for one of the resources that would be packaged up, say a Flexible Layout. When you then package this stuff up, it will include all attached resource data files, regardless of whether the attachee resource actually uses these files or not.