The first link in the previous post is fairly OK.
The important thing is to set a password for the "user" account on the N9, after that you can ssh to the device as user.

Normally to connect, then you can insert a cable to the USB port of your N9, and select the SDK mode. When you do this, N9 will show up as an IP device on the USB interface.
(provided your computer has the right drivers installed, I don't know about what you need in windows but in linux it's fairly automatic)

What I like to use myself; When I am at home, my N9 is always in WLAN. I just ssh to the device using wireless connection, where-ever it is, on the table or in my pocket.

About fixing the problems, usually you can look at log files, or top to see if some program is misbehaving and then just restart it with a KILL signal.
You can also reboot the device via a command, that should fix any normal jammings