Sorry if I am telling you things you already know, but I'll give it a shot.
when they say 3rd and 5th they are talking about the notes of the scale. The C Major scale goes
C -root
D 2nd
E 3rd
F 4th
G 5th
A 6th
B 7th
and back to C the root. of the scale.
So if you start on the C that is at the 3rd fret of the A string, the E that is the 2nd fret D string will be the 3rd, and the G at the 5th fret A string will be the fifth, Also, scales go the other way, so the G at the 3rd fret of the E string is the 5th and the Open E is the third.
Those positions make a pattern you can move anywhere on the fretboard just by moving the place you start the scale. so if you slide up from the C to the D on the A string, the 3rds and 5ths will be in the same places relative to the D as they were to the C.
The reason you play them so much is that they go together (root, 3rd and 5th) to form a major triad, which is a really basic chord, and they sound ok with pretty much every chord played in a major key.
An example of 5ths is pretty much every old country or rock and roll song from the 50's or early 60's
I walk the line
In that you can hear the bass player playing that sort of Oom-Pah line, what he is doing is playing the root note of the chord, then dropping down to the 5th note below, which just happens to be down a string (towards the thicker strings)
as far as playing them too much, It would depend on what you are doing, I'm still a beginner myself so I'm not so hot at coming up with lines other than if I am just screwing around, so I dont have much advice to give, other than listen to players you like and see what they do.