Music theory applies to music regardless of what instrument one plays. Sure, there are specific areas of technique that can be unique to each instrument with some similarities between some instruments (guitar to bass and/or violin to mandolin, etc...) and there are a couple differences in how various cultures and regions create/express music (eastern hemisphere's use of quarter tones and/or atonal music) but the theory of music is pretty much what it is.
Going up and down the neck with ease...let me see if I can break this down for you...the music notes we use are as follows:
A- A#/Bb - B - C - C#/Db - D - D#/Eb - E - F - F#/Gb - G - G#/Ab - and back to A and repeat.
That's only 12 notes, right?
Now check out your guitar:
probably got 6 strings and maybe 22 frets.
6 x 22 = 132 different notes, right?
Sort of...it's really 132 different places to play just those 12 notes so that leaves room for a lot of repetition...redundancy.
To me, the key to going up and down the guitar neck with ease is to discover how those 12 simple notes repeat themselves across those 132 different places and you can start to do that by recognizing scale patterns (both by shape and by interval structure) and chord patterns (again, by shape and by triad structure) all over the neck.
It can start with learning 1 scale in as many places as possible or learning a chord as many places as it occurs then start moving around little by little, adding a new scale and a new chord, etc...
Bottom line is it takes time and practice.