Okay, I am reading through this bit by bit to figure out how to respond to you, but basically:
Yes, a package can have multiple sources... Which one is used, depends on whether the package is being built by MakeRelease (the source package), or being installed by the system (ConfirmDependencies), we currently use the Pluto Ubuntu Addons source for most of our stuff, but you can use an external URL source, etc, to download the package from elsewhere. Which ones are apropos still...need to be documented...
This whole system forms an abstraction so that later on, other linux distributions and other platforms can easily be coodinated, MakeRelease can build the appropriate packages for a given distribution, and ConfirmDependencies can automatically install for the right distribution.
Take note specifically of the individual folders, and their file components, note that you can use wildcards, but also note the use of the flip source checkbox. Binaries use it, source packages do not. It alters how the path fields are parsed. Pay attention and notice that the paths basically pick up where the paths in the sources area leave off.
As for miscellaneous files, notice that there are mkr_foo.sh scripts typically put there. This can also be used to install boot scripts into their appropriate places, etc. There are mkr_ scripts for preinst, postinst, prerm, and postrm. This is where you do any configuration required by the package that may be required like, setting it up as a system service, whatever. Look at examples of mkr_postinst.sh etc in the individual packages in src/ in the SVN.
-Thom