In this example code, would I replace the 'H' with a 'L' (for left eye) then have make a similiar if statement for the right eye?
No, that example is crap.
if (mySerial.available()){
c = (char)mySerial.read();
if (c=='L')
{
redvalueL=BTSerial.read();
greenvalueL=BTSerial.read();
bluevalueL=BTSerial.read();
}
Likely, this code won't even compile. But, think about what this is doing even if you change BTSerial to mySerial. If there is at least one byte of serial data, read which eye the byte is for, then read the next three bytes which most likely haven't arrived yet.
Not a good idea.