I agree with Dave, it can take years, and there really are no shortcuts, but hopefully, you'll start noticing patterns between the note positions. Such as how your octaves fall, where your 4ths, 5ths, etc. are in relation to your roots.
Other than that, it's all memorization.
Good news, though: there are only 12 notes to learn! After that, it's all repetition.
I'm assuming you know your alphabet: A - A# - B - C - C# - D - D# - E - F - F# - G - G#... and repeat.
That pattern will never change. If it helps, draw your fretboard, and list the notes so you have a chart in front of you.
Hope that helps a bit.