A distinction that is often lost (and confused me at first) is that SmartOS is the whole banana (the global zone) while the userland/guest OS is often referred to as a SmartMachine. The documentation at smartos.org tends to focus on the former, while if one is looking for documentation on the latter, the best place to look is at the Joyent Cloud documentation. Of course, Joyent Cloud docs include a lot of stuff about how to manage your collection of SmartMachines via Joyent's management web interface (which you won't be doing if you are playing with SmartOS at home), but userland and package management stuff, database hints, security, etc. are all there.

SmartOS docs

Joyent Cloud Docs