I am not 100% clear on whay you mean by manually monitor and switch valves.
A. You need to have a pause in the program until you adjust some valves by hand, at which point you say go and let the program take over?
B. You want to programmatically adjust valves until you are ready to say go and let the automated routine take over?
C. You need the program to detect what is the current state of the valves and initialize itself accordingly?
I'm guessing you are thinking of B.
You should definitely look at the state machine architecture. But you may not need anything even that sophisticated. Perhaps you just need a 2 frame flat sequence structure. In the first frame you put the while loop as you described in your message. Inside of that you do whatever you need to do whether it is scenario A, B, or C as I listed above. Then you could have a button called "go" that when it's pushed, its true output is wired to the stop terminal of the loop. Once that frame is executed, it will advance to the 2nd frame of the sequence where your automation as you already have it in your attached VI is executed.