Issue: When Synaptic Package Manager is present on a system, its launcher is not imported into the Xfce graphical Settings Manager. As a key application to explore and modify the system, its presence in Settings Manager seems logical. (In fact, the package sources manager is present, but not the package manager itself. This seems inconsistent.) Solution: Make Settings Manager create or import a launcher for Synaptic Package Manager whenever the latter is detected on a system. -- System: Xubuntu 13.10, 32 bit, fully patched.
This is up to the developers of Synaptic (they need to modify the categories their .desktop file holds) or your distributor. Xfce can do nothing about this unfortunately.