Hi there,
i have some suggestions:
do practice some scales up and down the neck, not just patterns but vertically and horizontally(up and down one string). you could do that with just the major scales. it would be good to be reading the notes as you playing the scales just to get used to the connection between notes and fingerings.
then after that try to play scales in different places not just what you are comfortable with.
after that start learning some simple melodies like Christmas songs or nursery rhymes because you know these tunes best so you would know if you have played it right or not and again do have a reference or read off some scores.
if you do need a book, hal leonard has some good books for reading on the guitar.
or alternatively you could get a classical guitar book and start learning how to read notes from there, you dont have to learn classical guitar but at least its a tried and tested method to reading notes.
lastly, where to play certain notes esp for the guitar really is about personal preference sometimes or convenience like for example a 'closed' note sound versus an 'open' note sound.
let me know if this helps