suggestions to reduce Soft Doors upper doors from making noise and flapping against frame?

I'm assuming you're referring to the after market soft doors as offered by Bestop. These are nothing more than a basic rod frame with fabric coverings more commonly known as Skins. These doors were not designed to be water or air tight. However there is a protocol when installing these doors. One must "Knee" the door and pull the top half of the door towards you. This would then create a more secure fit or placement on the jeep's body. If you want a better seal, you have 2 options. Buy full metal doors or factory half doors w/ molded plastic/ fabric tops. The molded plastic in conjunction with the fabric outer skin and seal does fit tighter as compared tot he lesser rod/fabric design.