I'll second the suggestion to track these funds by class...it will make it easier at the end of the year to adjust any restricted equity accounts so you have a permanent record of how much each fund balance is. 

This is how I handle fund accounting in QBO. If your different funds just need to be tracked separately, I just set up a class for each, and make sure to designate the class each time activity occurs.

If you're needing your books to adhere to GAAP accounting (i.e. separate treatment between Unrestricted and Restricted) I still use the classes mentioned above, but I'll also set up an Other Income account called "net assets released" or something similar, and each month/period make an entry to this account to zero out my net income for all the restricted activity, with the offset being the restricted equity account matching that fund on the balance sheet. This way, your P&L is appropriately tracking both the inflows and outflows of your restricted activity on your P&L, and your equity section of the balance sheet shows the correct balance of each fund.