I've made the following changes, which I think work very well.;
Preferences -> Plugins -> Device Interface Plugins -> Kindle 2/3/4/Touch/Paperwhite Device Interface
Click customize Plugin button
Make sure azw3 is checked, and move it to the top of the list with the up arrow, so it becomes the prefered format. (azw3 is amazon KF8 format, wheras .mobi can be either or.)
Optional: I've actually unchecked mobi for my kindle, since I want Calibre to convert any mobi to KF8. Amazon has made many improvements to the KF8 reading software over the old mobi/prc. and a KF8 file will work better. In particular, page turns are much faster (especially turn page backwards which is painfully slow on movie files) and images can be opened/zoomed in image viewer.