Long story short: Overlays and Video Links are an integral part of the Hypervideo and shared by all users, Annotations are user-specific additional materials.
FrameTrail enables you to adjust the player layout to your specific needs. The layout can be configured at several stages:
By simply clicking the areas, you can toggle the display of certain features:
(this only affects the player layout, all features will still be available when editing)
This setting defines how Annotations and Video Links are displayed when activated (either by clicking the squares in the timeline or scrolling up / down in the player):
The Hypervideo "adjusts" its size in order to make room for Annotations or Video Links
Annotations or Video Links slide over the Hypervideo and thus "overlay" the main video area