The flashing needs to be grooved into the log course above doors and windows, and everywhere that a roof attaches to the log structure, such as over porches, sunrooms, and the like.

This diagram shows how it is done in a Barna Log Home, although the procedure will be similar in any log structure. Our Barna builder did not prepare for flashing, which is (apparently) the homeower's responsibility after-the-fact.

Here is a pdf of this same diagram.