It's very difficult to answer this question, because before knowing the how? we need to know the why?. Remember: at any time, at every point, in UX context is everything.
For example: why do you need to track views and or clicks?
This is the paramount question, and knowing the answer to this question will probably give the answer to your specific question, which is just a subset of the main one.
Let's take a look a different scenarios:
In this scenario, you need to track a focal point of the video, and how the user interacts. Then you'll obviously need to track the click, the view is anecdotic since you have no way to know if the user effectively watches the video.
- You need to track views between lengths
In this case the system has to assume that any annotation contained between
video_length(n) has been watched. If you look for more accuracy, you can add a control at the end of the video to know if the user watched the video or if the video was abandoned playing, although this is not very likely
- You need to accurately know what part of the video has been seen
In this case, you can do something like segmenting the video lengths based on annotations. Thus, if user started on A1, when video gets to A2 it should stop and require user interaction. Then, if user chooses to continue, you'll know that s/he chose to watch both segments and intentionality is clear, thus you can count both A1 and A2.
- You only need to track video views, whether partial or complete
In this case (the most common one), then you don't need to worry, simply count how many times the video has been played and that's it
- You need to take track of the point where the user chose to enter the video
Here you will only need to track the click on the annotation
These are just a few examples of possible approaches, keep in mind that your case could be within these parameters or be something totally different (for example, for more scientific methods you'll need additional control mechanisms). The point is: as long as you know the why? you'll be closer to the how?