this is just my few cent worth of advice, and this what really helped me from what i was taught from my sensei and it really showed me the light.
Yes at first you must memorize them. but after awhile it will dawn on you that they become second nature.
and by second nature i mean, if you look at your fretboard and say you start a note on the 6th string everytime, Like how you would find the root notes to the 5 pentatonic shapes, you will realised that its the same pattern for all keys. the Root notes in each pentatonic position will show you relations to the chord shapes, Thus the CAGED system. once you see the CAGED system, ALOT of things is possible, like you can start your scales there, arppegios, your chords in all different positions.
this is jus a method and a system that can help you to rock out. but like what the others have said, this is jus a SYSTEM to help you see, at the end of the day you will still need to have your ears open. to be able to hear and play what you hear. and put rhythm into whatever you are using be scales or chords.
And to practice smart on knowing your notes is to start practicing your notes in C major scale. Cuz all the notes in there are natural notes, once you noe your natural notes, your Sharps/Flats is jus a shift up or down your frets.
hope this helps. cheers! \m/
P.S: I am just addressing to the importance of knowing your notes on your guitar, but overall you will still need to learn things like power chords, major minor theory etc etc, and of cuz use your ears and feel of a song to play a rock tune you hear. but knowing your notes will really help alot more when you learn those things when the theory sits in. you will be able to apply things a lil faster.