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Last question how can i tell when i can play a chord within the scale. For example if I'm playing through AMaj scale
A-B-C#-D-E-F#-G#-A and I'M using this progression is the only time i can use the Amaj Chord is when I land on the
A-Note. For example if I pick A-B-C#-D-E-F#-G# the next note being A is this the best time for me to use an AMaj chord?
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You can play any of those notes over the A maj chord. Try it out. Have someone repeatedly strum an Amaj chord and play those notes over that chord. If you play any of the notes from the A major scale over the A Maj chord, you will find that they all sound "appropriate" over the chord.

As for your chord question, all Chords, Major, dominant, minor, diminished, etc... are created based upon certain formulas. Those formulas, almost always can be derived in some way from the "plain old vanilla" Major scale. Its just a matter of learning the formulas for the specific chords you want to play and how they relate to the major scale.

In some cases, those formulas use only the tones contained in the Major scale. For example, the Major 7th chord -- uses the 1st, 3rd, 5th and 7th tones right out of the Major scale. In other instances, those formulas require you to raise or lower one or more tones of the Major Scale. For example, the Minor 7th Chord --uses the 1st, and 5th tones right out of the Major scale, but requires you to lower or "flat" the 3rd and 7th tones by one half step, making the chord formula: 1, b3, 5, b7 for that chord.

There are other ways of looking at it, but I find that it is less confusing to just use the Major scale as the building block for everything that you do. Check out this website I stumbled upon a while back:

http://www.looknohands.com/chordhouse/

It should help you out to some degree with the different formulas for the different chords. And it will show you just where all of the notes for those various chords are on the guitar neck in any key.