Consider not-changing your graph representation right now. It sounds like it isn't a real issue, at least at the moment.
If you decide to not change your graph representation, also consider writing your code in such a way that *if* you did change it, that it would have a minor impact on the rest of your code. This means that you would use some sort of abstraction to access the graph. (like functions or class objects)
To keep it as simple as possible for now, consider using functions to access and modify the graph, instead of i&j indices into an array. If you change things later, you won't have to modify (much) the routines which are accessing the graph because the function calls would stay the same. This might also give you the opportunity to "factor out" all the stuff you keep having to do with the graph to get work done.