Here's a good exercise: grab your guitar, decide on a note, let's say Eb for example. Now, as quickly as you can, try and find that note on each string, including the octave (above or below). Do that a few times and take a break. Then come back to it, and do the same thing again. Pick a new note and repeat the process.

The point is for the process of finding any note to become automatic, so you don't have to think, in order to find the notes. It takes time to get this all down, but it's well worth it. Be patient, and try to learn only a few notes all over the fretboard the first few weeks. Get these down "deep inside", so finding the note on any string is instant. Go back to the previous notes you learned often, to make sure you really got them "down".

I'm not a big fan of the CAGED system personally, but I know a lot of guitarists have found it useful.

If CAGED helps to learn the notes as well, by all means use it. Both these techniques are just that, techniques for learning. They are just vehicles for getting you to where you want to be.