Learning what “up or down the neck” means is one of the funniest things about learning beginning bass and guitar. This has perplexed and embarrassed more adult students then almost any other point! (Almost…)
Musically, the words “up” and “down” most often refer to pitch. “Pitch” is the highness or lowness of a note determined by how fast the string is vibrating. (More about pitch at the glossary at my website.)
An open guitar or bass string vibrates at a certain speed. When you press the string down to a fret, it shortens the string thereby making the string vibrate faster and the pitch higher. When you play notes going from the head of the instrument towards the sound hole, or pickups, the pitch’s are getting higher and is called going “up” the neck. Using a vertical guitar as an example, going up the neck is going down in gravity, and going down the neck is going up in gravity! So down is up and up is down!
It can take a while to get used to this when learning to play. Often enough I’ll say “move your finger down one fret” and the student moves it according to gravity instead of pitch, laughs then corrects the motion. This becomes rather humorous after the 20th or 30th time it happens. Some people get used to this after a few weeks, though most actually take a few months to stabilize this concept.
After all, we’ve been dealing with gravity longer than dealing with vibrating strings!