i would say, that no you do not want to use apt-get upgrade, as opposed to checking for updates in blue pill mode with the app manager.

just before the newest firmware (skype enabled) came out i did just that, and it seems that there were newer versions of things checked into the repositories that broke dependencies and had issues.

i wound up losing certain functionality and could not do things that i was able to perform before the upgrade. i cannot quantify the issues i had, at this time, because i reflashed afterwards and have since upgraded to the newest firmware as well.

the benefit to the apt-get command line utility is the ability to add non standard binaries to the device, that are mostly used from the command line. the normal apps usable through the GUI are best upgraded or installed with the app manager.