How to annotate specific parts of video in pre-production?
Disclaimer: You didn't specify what program you are working with, so I assume you are using the current version of Premiere Pro.



Assembly Workflow

Your workflow is a common one for beginners. Back when I gave Premiere Pro introductory courses, I noticed many students start out like this, basically doing the assembly, cutting and arrangement of the footage completely in the timeline. While there's nothing wrong with that approach, you can significantly speed up your workflow by seperating the initial material assembly/screening1 and the actual cutting. 

The assembly is where you look through your material, sort and rate/tag it so you know what you are working with and can find specific parts of your material quickly. Mastering the project panel and all the sorting/marking options is a large subject on it's own, so I'm just gonna give you an overview of my workflow and the sorting options I find useful.


Workspace. Under Window → Workspaces, select Assembly. This workspace is optimized for assembly and material screening, it's just easier to work with. You can also rearrange the panels and save it as a custom workspace.
Bins. You can create bins to sort your footage into by pressing CTRL + B while the project panel is in focus. They work similarly to folders on your computer, you can drag your video clips and other assets into them for sorting. For example, you can create seperate folders for every scene in your movie, a seperate folder for B-roll material, a folder for music and other non-video assets et c. You will have a much easier time finding specific clips after you have sorted them in this way.
Color labels, Star Ratings &amp; Keywords. You can use several variants of marking systems if you use the Metadata Display options. For example, I like to use colors labels to mark the best clips and the rejects. Once you have set those up, you can also use filters or sort by color labels to find the good stuff quickly. Other options include Star Ratings (that you can assign shortcuts to), Keywording and several other editable metadata options. I've already written some other answers on this, so ... 


Quick setup for Star Ratings
Setting up Keywords and other Metadata options

List and Thumbnail Views. On the bottom left of the project panel, you can switch between the two views and adjust the size of the item display. While in List view, you can rename your assets from the generic filename (like MVI_0817.mov) to something more useful. I like to use a consistent naming scheme so I see what every clip contains at one glance. For example, if you name your clips [scene]_[shot]_[angle] (e.g. garden_establishing_panorama), you can find a specific clip without even looking at it.
The thumbnail view is useful to get a feeling of your material and quickly stitch clips together that fit. I usually open a second instance of the project panel, set it to thumbnail view and put it on my second monitor. It's great for quickly sifting through your clips and finding the right one for your scene. 
In- &amp; Out-Point, Markers. This is the most important part of this workflow, and the answer to your initial question (got a bit carried away with my answer). You can mark the In- and Out-Point of each clip by pressing the I (In) and O (Out) Keys respectively. This will add those points at the current playback position in the source panel (they are not temporary, so you can add In- and Out-Points to each clip in your project without dropping any of them in the timeline). If you have set up those points for a clip, only the portion of that clip between them will appear in your timeline when you add it to your sequence (you can of course adjust the start and end point in the sequence using the cutting tools as usual). More information on In- and Out-Points and quick ways of adding clips to the timeline can be found in my answer here.
One problem with this method is that you can only use one In- and Out-Point per clip. So if you have one clip that contains two parts you want to use in your movie, you have a problem. There are two ways to deal with this. 


Markers. You can add markers to your master clips in the source panel by pressing M. The marker is added at the current playback position, you can change it's color and other attributes by right-clicking on it and selecting Edit Marker… from the context menu. However, this option is somewhat limited, since you will still have to manually adjust the clip length in the timeline, the marker only provides a visual aid. 
Subclips. If you have set an In- and Out-Point for a clip, you can create a Subclip from that. Right-click on the clip in the project panel and select Make Subclip from the context-menu. This will create another instance of that masterclip in the project panel limited to the boundaries marked by the In- and Out-Point. This way, you can split up a large clip into several subclips, each containing only the portions that you need. The downside of this is that it's somewhat tedious if you have many long clips.  



This workflow works best if you film your material in a certain way, which will also avoid the problems with In- and Out-Points mentioned above. This leads me to the following point.

Good filming habits

In general, try to film in a way that will make the assembly/screening of the material much easier and streamlined. This mainly means two things: 


Press the record button only after you have composed the shot. If you point the camera in some random direction, press record and then compose your shot (i.e. position your camera/subject), you will have a few seconds of unusable material to cut from every single clip. And, even worse, the thumbnail view of the project panel will be mostly useless, since the thumbnails won't show the actual shot. If you start the recording after you are done composing your shot, the thumbnails will show you at one glance what every clip contains, allowing you to cut much faster. 
Start a seperate recording for each shot. Many beginners make the mistake of just letting the camera run while they film, resulting in long files that are tedious to check and cut. Try to seperate the video files by stopping the recording and starting a new one for every shot/angle. This way, you only have one relevant part per clip/video file, allowing you to work faster with In- and Out-Points and the other Metadata Display options mentioned above. Also, try to make each recording only as long as you need it to be. For example, if you shoot a couple of B-roll shots from the same vantage points, do not just press record and proceed to point your camera at everything. Instead, compose the first shot, press record and record for 5~10 seconds (no longer for B-Roll). Then stop the recording, compose the second shot et c. This way, you end up with a couple of short, concise clips that you can assemble and add to your movie quickly.




This is all I can think of at the moment, though there's definitely more to say about this subject. I haven't even touched the actual rough and fine cutting yet ... but this answer is really getting too long, so I'll leave it at that. If I forgot anything important, feel free to inquire in the comments or ask a seperate question, I will be happy to edit my answer or add a new one if necessary.



1 Not sure what the right term is. In German it's called (Material-)Sichtung, which translates to sighting or screening of the material.