My first recommendation is keeping two copies of any wiki pages you are using to present your non-linear design work. One is for you, and whatever creative madness you need for your design process. This one is hidden from the world, like a corrupt accountant's second set of books. The other is the one you present for feedback and follows many rules and conventions, some of which are project specific and some of which are mentioned here. Keeping two copies of your pages will allow you to edit and update your presentable version of the information you want to share without losing easy access to the personal reminders, references, and inspirations that helped shape your design process.
Here is a logical proof for the statements in the preceding paragraph:
A: A good designer puts more thought into their work than is immediately obvious.
B: Anyone who puts more thought into their work than is immediately obvious is a corrupt accountant.
C: A corrupt accountant keeps two sets of books (i.e. two copies of every page).
A+B+C: A good designer keeps two sets of books.
There is no defined etiquette for how a mission flow chart should be styled, but try to be consistent above all else. Use colours to enhance clarity but avoid a rainbow of colours - excessive and clashing colours are distracting. Many Visio themes have a set of 6+ colours that go well together. Try to stick within these or use a colour wheel (color.adobe.com) to create another small, complementary set of colours to use for your mission flow chart. Do not use the same flow chart representations for arcs that are both mandatory to complete and arcs that are mutually exclusive. Use diamonds or another distinct shape to show "and/or" logic to help avoiding the same flow chart representation for any situations that might look the same on paper but would play out very differently in the final game. Remember that the chart should convey information that executives can understand at a glance without creating more confusion through poor communication. Communication is one of the many arts a great game designer must become proficient in because at some point all designs need to be approved by an executive, a publisher, or an audience of crowd-funders.
Don't have access to Visio? Want to create flow charts like this anyways? DO NOT USE WORD. Use Draw for free in the Apache Open Office software collection or other equivalents that can be downloaded online. Using word processors to do flow charts will waste your time. Furthermore, while using Draw you will be learning valuable communication skills and workflow efficiencies that can be applied when you do switch over to Visio, or any other professional flow charting software.