Its meaning depend on context. We still have a way to go means that we are not at our destination (literal or figurative) yet, so we still have further to travel/more work to do. Way to go as an exclamation of approval of someone's efforts is very informal (possibly American Eng) and is, I assume, a contraction of the phrase 'that is the way to go'. In other words what you have done is just the right thing to do and is achieving the desired results, so well done - you have gone the right way.