Muscle memory... In my opinion, is the hidden force that makes playing an instrument possible. If you have to use your brain to change chords it is because you have not yet attained the Muscle Memory to do so. It lies beneath the surface of all the stuff you do with your brain when you play an insturment and as such is easy to over looked. Then there is a sudden "break through" and you can play the part that was impossible before. That is usually a result of developing Muscle Memory.

You can't reason with Muscle Memory, you can't force it, or cajole it. It grows from hours and hours of practice. Those hours imprint the needed skills to reliable play what you are seeking to imprint into your fingers and spine. This eliminates all the time that impulse would spend traveling to your brain and back reducing the time needed to make a quick move from one chord (or note) to the next.

Faith is right about fingering the fret board (even if you don't strum the strings). You need to imprint those chord patterns into you Muscle Memory. So much so that your brain is simply not required (other than to pull the trigger on this riff or that chord). That, usually come form hours of practice. The ablity of any guitarist is a direct result of the hours spent practicing, NOT HOW MANY YEARS YOU HAVE DABBLED IN "PLAYING WITH THE GUITAR". Patient, Persistant, PRACTICE is how Muscle Memory happens.

Welcome to the long and winding road....