One of the things I have found helpful to learning the notes on the fretboard is the Google Android app Guitar Fretboard Quiz & Tuner. There is a free version, but for around $2 you can get the paid version. For example, it will randomly ask you to play an Eb on the 3rd string and listen out make sure you are playing the correct note. I find that random note questions are what helps me learn the fretboard, rather than just trying to remember the notes in sequence.