I have been playing guitar for roughly over a year now, for the most part self-taught, and have just recently started learning scales, however I am very confused on how the different notes that are contained within the scale relate to each other all over the fret board. Say the A minor scale; A B C D E F G. Am I limited only to play within a certain area of the guitar say from fret 5 on the 6th string to the 7th fret on the 4th string? I have attempted a few patterns of the CAGED method but I would much rather not get stuck inside of "the box". I know all the notes on the fret board up till the 12th fret moderately well and can find them without trouble, I just don't understand what I should do with the scales I've memorized and how I can piece the different octaves of a scale together to create an improvised lick or riff. How can I play and learn scales without having to forfeit my musical creativity to a box pattern?
The scales you have learned are probably one octave. All they are is a group of notes that sound well in sequence - any sequence, depending on the chords they're played over. They have been put in that order because it's the sort of thing humans do. However, when you solo, you're not going to play just up and down those scale notes, you're going to miss a couple, play some twice, go up and then down before reaching the top note of that scale. You will even go above that top note, so it's worth extending your scales to two octaves and more.
In the 'boxes', you'll be able to get two octaves from bottom to top, easily. What you need to do to address your question is find the next note of a scale higher on a particular string, instead of what you've learned - moving back towards the nut and up a string.So, in the long term, you'll be able to run up and down scales, not necessarily in a 4 fret box, but up above it whenever you want. This way, you'll find other 'boxes', because, after all, that's the way guitars are designed to work!
Using this knowledge, you'll then be able to slide in and out of boxes, on the same string. Think about it, if you only know one box, some notes are slideable, but others certainly are not. That's where the next box (either side) comes into play, so to speak.
For soloing, you would want to look into the pentatonic scales, which consist of only 5 notes. There are 5 box shapes across the entire fretboard. Just a note here, major scales and natural minor scales are the same exact thing, the only difference is the root note. You should have a look at relative minors and majors for this, in short, the A minor scale is the same exact scale for C major, the only diffirence is the root note which will A and C respectively.
You are defintely not stuck to one box shape. It is very common to move between diffirent box shapes up and down the neck. For as long as you know where every note on the fretboard is and the notes of the scale you are playing, you should be fine.
In addition to the pentatonic scales, it is really a good idea to learn the 3 notes per string method as well. This is really helpful when playing licks. There are 7 basic shapes which is also spread out across the entire fretboard, so again, you can move across more than one shape when soloing.
I'm also self-taught, and uses a lot of tutorials from guitarjamz and guitarlessons365 found on youtube to learn stuff like this. Between those two guys, they have really good video tutorials on the pentatonic scales and pentatonic runs up and down the fretboard, as well as the 3 notes per string method. I really would recommend having a look at that
I would give the CAGED system another try. I felt like you and was somewhat trapped in the minor pentatonic box for years but actually the entire CAGED system lets you break out of that and shows you where the "right" notes are all over the fretboard. As others have said, it's generally easiest to start with the major/minor pentatonic scales, because as the name implies, there are only 5 notes in each octave, rather than 7 in the diatonic scales. Plus they are very common in rock, pop, and blues, and can get you pretty far.
The common 5 patterns of the CAGED pentatonic shapes all have two notes per string, and let you shift from position to position seamlessly. For instance, in E minor, you have the typical minor pentatonic shape starting with the open E string. Then you can move up a position to the next shape (see position 2. You'll notice the left half of the second position box lines up with the right half of the open poistion box. So it's all the same notes, just different places to play them. So using this you can walk up and down the whole fretboard, using the boxes or jumping from one to the other, and it's really anything but limiting once you get all the 5 shapes down.
Then there are the symmetrical lead patterns and these are really my favorites because they are symmetrical, so really easy to remember, and they let you move up and down the neck (and connect the box shapes) really easily.
If you look at Lead Pattern 1, it will be the minor pentatonic if you start with the 3rd finger on the 4th fret in the diagram. And Lead Pattern 2 will be the major pentatonic when starting on the 2nd fret with the 1st finger. But either one can be used for major or minor, it just depends on which notes you start on. Same for the boxes. With the Position 1 Box it's E minor pentatonic if you start on the first note. But the Position 2 box is G major pentatonic if you start on its first note (3rd fret low-E string in the diagram).
To more directly answer your question, you should learn as many patterns and different ways to play the scales that you can. Or you can just pick out all the right notes. For example, with Aminor, you can just use all the natural notes (A,B,C,D,E,F,G). So you don't even need to know the shapes since you know where all the notes are on the fretboard, you can just pick them out. But the shapes/patterns let us turn off that part of our brain that has to make calculations, and lets get into the flow of the music a bit more.
My favorite versions of the diatonic scales are the 3-note-per-string shapes. Especially the Ionian or major scale, which is very symmetrical and E/A strings are the same, D/G are the same, and the notes on B/E are all the same. The Aeolian (minor) and Mixylodyian (major variant) are also very useful for rock/pop.
One really important thing though that it took me entirely too long to learn, is that all of those notes in the scale are not equal. You can't just pick them at random and go up and down (well you can, but it won't sound as good). You need to learn about the intervals, and how they relate to chords. When to play the minor 3rd, or the dominant 7th for example. Learning arpeggios helps with this, because those are the "key" notes you want to focus on in most cases, the root, 3rd, 5th and sometimes 7th of a scale. Those are the notes the make up most common rock/pop chords, and they are always stable choices for the melody/soloing.
As a guitarist, you can't really avoid "shapes" or "boxes", since a lot of what we play is arranged in those terms. The key is to know where the boxes are, and also how they relate, and what the feel of each note within it is.