Many of our QuickBooks clients use class tracking to keep track of restricted funding and project activity. When it comes to salary costs, it can get tricky and time consuming to allocate these costs across multiple classes. One trick is that when entering the salary expenses, you can put these all in the General (core) class initially. This helps you get on with the bank rec and other things that are more interesting!
Then at the end of each month (or quarter) you can do a journal to move (allocate) these costs across your classes in one go. In the journal you would credit salaries/general class on one line and debit each other class accordingly
This template can help you work out the numbers. It is just a suggestion - there are lots of ways of doing this so feel free to edit this as you need. For example, the template uses percentages, but you could do it by hours if you prefer. Just click on the links to download the tempalte and the worked example.