If you are going to use our recommended option that includes bonding the skirt to the frame you are going to follow these steps below. The key to coming out with a nice looking end result is going to depend on how much time and effort you put into your prep and cleanup.
Please note that you must also use screws. The 3M 5200 specifications note:
5200 is not recommended for the installation of glass, polycarbonate, or acrylic windows that are not also mechanically fastened. Inconsistent adhesion of these un-primed substrates, specific design of the window and movement due to thermal expansion and flexing may cause application failure.
See full manufacturers specs here: 3M 5200 Tech Specs