I can relate to what you are saying
When starting to use the NCE pack it can seem a bit overwelming indeed. We are still looking for the places where the information is located and in some cases if the sample of opportunities for a spot is small the information is still not very accurate.
After your database starts to grow as well as the number of hands on the players things will start to make more sense and the places to look for the specific notes/popups become second nature.
To help overcome these first steps make sure to have a read through the .pdf files in the "NoteCaddy Coaching Pack Files". Specifically the ones that describe how the HUD and definitions work and are organized. The "Ultimate Definitions Explained.pdf" is the one that describes this the best.
Depending if the poker room you play on allows to use badges you might want to have a look also at the "Ultimate Badges Explained.pdf" to better understand what the badges mean and how to use them. Something I learned while using Notecaddy is that reading through this document also gives you some insight on possible spots to try out even if badges are not allowed to be used.
When a note has enough data points it produces a much better insight not only by the hand notation with the cards shown but also with the stat percentage that also shows in the notation. Understanding how to quickly read a note by looking at these two points is key to make good use of Notecaddy.
A good way to train for this is by going on the hand replayer and reviewing some hands of the players you have most hands on so you get a good sample on most notes. Play around with the HUD, look at all the popups and notes so when you are playing live you can focus your attention quickly on what is important to look for.
Also have a look here: http://notecaddy.com/How-to-read-a-NoteCaddy-note.ashx
Bookmark that site as well as it has a lot of important information for a Notecaddy user.
Let us know if you have any doubts.