It may also be helpful to keep a list of page numbers on which each color of highlighter is used - this can then be graphed to show the pattern of occurrences in the story. (Since you're writing a game you may prefer to do this with a game script, but you would need to first 1) find a game that actually has a good plot, a difficult task in and of itself, then 2) find or make a complete transcription of the game including descriptions of all cut-scenes. Similarly, you could do this to a movie script if you had one complete with stage directions.)
But what am I supposed to be highlighting? o.O
1) Well for starters you should take your post-it bookmarks and mark the initial incident, the climax, the resolution, and any major complications or reversals. Now you can see how many pages this story allots to each section of Freytag's pyramid.
2) Now, taking more of a plot snake or grammatical tree approach, you can go through and mark every time a character comes to a resolve, or a character's attempt comes to success, failure, or complication, or an outside event occurs which affects the plot.
3) You could, if you wanted, go through and color each place where one of the book's themes is developed.
4) You can mark which sections are from each character's point of view, or how the book switches between two types of material (such as main story and flashback or myth or comic interludes).
Etc.) Or anything else that you are having trouble with writing.
Because a lot of authors have trouble with plotting, they have devised many methods to help themselves tackle this problem.
The Dramatica program and associated theory books are probably the most complete and automated plotting aid - and also the most confusing and time-consuming to learn.
The book 20 Master Plots is less flexible and automatic, but simpler.
If the book you want to imitate the plot of happens to be a classic you may find that Cliffs Notes may have a plot outline of it, or its outline may be contained in one of several books that are collections of plot outlines of classic novels.
Then there's the Gary Provost paragraph, which is a mad-libs style approach to describing your whole plot in one paragraph (and only works for certain types of plots). Just take the following paragraph and replace all the generalizations with details:
Once upon a time, there was someone who had a need which had been created by something in his past. Then something happened to him, and he decided that he would pursue a goal. So he devised a plan of action. and even though there were forces trying to stop him, he moved forward because he was very motivated and there was a lot at stake. Just as things seemed as bad as they could get, he learned an important lesson, and when offered the prize he had fought for, he had to decide whether or not to take it, and in making this decision he satisfied his need and laid his past to rest.
There's also the notecards method, the cover-a-wall-with-blank-paper and draw your plot on it method, the 3-, 5-, and 9-act play structure methods, and the just-start-writing-and-tighten-up-
the-plot-in-the-second-draft method. Experiment and see what works best for you. :)