What I did to get to know my instrument was to learn all the modes that start from the Ionian mode (Major scale).
Go to a simple tonality, like C or G (the low notes on guitar) and play the Ionian mode (In guitar you can play it for two octaves in one (or a bit more) position), ascending and then descending.
After you've played it, go to the next mode, Dorian. It will start from D or A respectively and repeat the same process. Then go to the next one, etc. When you reach the Locrian, go back to Ionian!
These basic 7 modes are easy to find online. It's also easy to remember the shape they are creating, so you won't have to remember the notes.
After you've played all the modes up and the down the neck of your guitar, you can go to a different tonality. Go to Db, E, F# or something. This way you'll see where your weaknesses lie.
This is how I learned where the notes in the neck are.
Another thing you can do it to play the scales/modes in one string.
Also, you can play a scale/mode for two octaves like so:
- First octave in one string, second one normally.
- First octave normally, second in one string.
- First octave in two strings, second in one
etc. You yourself can find many variations of these.
Another thing you can do is to take a song you already know how to play in a certain position and play it in another one. For instance, do you have a song with the open chords D,C,A,E? Take it and play it without any open chords. Or you can play it an octave lower/higher.
Also, you can take a song you already know and transpose it in another tonality, like you did with the modes.