My Charles ran a few beads along the bottom of the door frame and then set the flashing box along the bottom of the sill.
The membrane went across the box and folded over the edge, making more of a "slide" for any water to go. Then the flashing was taken up the sides of the doorway three inches, causing a seal and further keeping any potential moisture from penetrating the house.
Make sure to take your time with the leveling. Each door frame and each door are slightly different, and if it's not level, the slider won't open and close properly. We checked the sides, top, and bottom until everything was completely level. Then we finished tacking the door into place, putting a nail into each hole along the sides and bottom.
The slider instructions said that the installation would take an hour and a half. With shimming and checking level, it actually ended up taking us five hours. Then again, we're not pros, just two weekend warriors trying to fix up our house.