Final Cut Pro Browser
Bring the same principles that you used in organizing your hard drive for the project into your project file. The Final Cut Pro Browser is where your media is listed in your project and you want to make sure that you label all clips correctly, put them in Bins, and then label the bins in the same way that you did with the folders on the hard drive. It is good to separate clips by scenes, shoot days, file types, or contents depending on how your project works.
Your Sequences should also be organized in appropriate folders, maybe even labeling them specifically and then placed into a Bin of their own in the Final Cut Pro Browser. The same principle should go for nested Sequences that include segments from larger Sequences, but these may go into a Bin specific to a scene. In general, you have to apply your own editing organizational plan to your project ahead of time and then utilize the available tools in the Browser to achieve these.
The Browser also give you the tools to label your clips even further, and there are a lot of informational blocks in the right hand columns. Here there will be a lot of different pieces of information about your clip or Sequence, such as audio, frame size, vid rate, data rate, compressor, and so on. You can also include your own information in columns such as description, scene, shot, take, angle, and various comment columns. These will allow you to quickly identify clips, and may be a good place to transfer some of the information from your assistant camera log.