Does the flight suit have to be one piece to be 501st approved?
I found this link, but it doesn't say anything about that.
501st Legion: Vader's Fist
I think if it isn't a one piece, the armor and other parts have to cover it up so you can't tell it's a two piece. Not for certain though...
It does not have to be a one piece. The two pieces are easier for some folks to make look right since guy can pull up the pants and tuck in the shirt. They'd specify it if it had to be a one piece.
I personally would like to go with a 2-piece because I just don't find one piece suits comfortable. I'm 6'4 and its hard to find one that doesn't look stupid on me.
The Lucasfilm suits were one piece, with the neck seal attached to it.
Flight suits, based on what I could find, are by definition, one piece.
The CRL for ESB Fett ( for example) calls for a flight suit, and gives details about the sleeves, pouches , etc. It doesn't say that you can substitute pants and a shirt. I'm sure that you could, if there were a medical condition of some kind. As a GML, I would only approve those that had a one piece suit, unless there a special circumstance. If a flight suit isn't comfortable, this may not be the costume for you. I'm overweight, and while the costume has gotten a bit snug, it's still comfortable. This has prompted much needed bike riding and food plan change to better be a Fett!
As Stormtrooperguy has said, don't stray from accuracy.