Simplicity - While there is nothing form stopping you in making one massive graph for you game, it is much better to makes multiple graphs that work together by breaking up your game's logic into graphs that focus on one (or a few) things.
Reuse - By creating Nested and Prefab graphs, you can re-use your graphs as many times as you need to. It also means if you fix a bug in the graph, that fix is applied everywhere that graph and graph logic is being used.
Back Up - While not directly a uScript thing, you should always backup your project in case of data loss, corruption, or accidental overwriting.
Comments - Use uScript's comment fields and comment boxes to help describe your visual logic. This will make it much easier to remember what you did (or for others to understand your graphs). Every node has a Comment property that you can use, or use a comment box to wrtie and color code a bunch of information (hold the 'C' hotkey and left-click on the Canvas to quickly place one)
Read This Guide - There is a lot of helpful information regarding uScript found within these pages. It will be well worth your time to read the whole thing and become a true uScript expert.
Ask Others - If you are having trouble, you can always ask other uScript users on the forum here: http://uScript.net/forum