Whenever I have to plot a multi-path story, paper, assessment, etc., I draw it out as a tree. Draw a line to represent your initial scene then draw a line for each choice that branches off from it. Then do the same for each subordinate scene.
On a separate sheet of paper I write a short blurb of what happens in each scene and correlate it to the tree with a number system. For example, after the initial scene, if you provide the reader with 3 choices, I dub the options 1, 2, and 3 respectively. Now suppose you select option 3 and you plot two more choices for the reader and you want to focus on the second. I would dub that 3.2. I continue to follow this pattern, so I can relate where I am on the tree by using the numbers.
This helps me organize my thoughts for each main path of my story and allows me to visualize the connections. The downside is the string of numbers can get rather long if you have a long story.
It helps if you already have an idea of how long you want the story to be and the number of main pathways you want the story to have.
I hope I explained that without being too confusing and hope it helps.