The packages I build, be it Transmission, Midnight Commander, or SABnzbd, are all installed using the same layout.

A new directory in /usr/local/ name by the package name is created. It contains all the files related to this package. If the package has some run time data it manages by itself, a second directory is created in /usr/local/var/ with the same name. This second directory eases the upgrade process: this is the only directory which is kept during the package upgrade. One notable exception to this is Transmission, whose data are stored in /usr/local/transmision/var/ for historical reasons. It was the first software I packaged as an SPK, and I did mistakes.

In addition to these directory, the DSM Package Manager creates a number of directories as explained here.

I choose to install the softwares in /usr/local/, as proposed here, page 12. It’s also close to what you can find on a standard Linux installation, keep a clear separation on the programs and the user data (in /volumeX/). The directories in /volumeX/@appstore/ and /var/packages/ are only used by the DSM package manager.