J. K. Rowling used an interesting tool. There is an image of this on the internet at http://www.mentalfloss.com/blogs/archives/73653. (Google J K Rowling Plot Spreadsheet.) She made a huge paper chart, which you could implement in an excel file if you were so inclined. Each row of the table is a single month. (You could use a week or a day as needed.) She had a column for each character (e.g. Ron, Hermione, etc.). In each cell of the table, she recorded what the character was doing at that point in time.
It occurred to me that a chart like this could contain far more detail than is actually presented in the book. You could fill in the chart first, and then choose which details to include in your narrative and which to leave out. For instance, Hermione appears out of the blue with some polyjuice potion at one point. Rowling chose not to include the process by which she decided to do this, found the recipe, overcame obstacles to making the potion, etc. On the other hand, Rowling had to giver her enough time to go through that process, so the potion appears late in the school year. You can work out plausible time lines this way.