Unrestricted:
   Administration
   Fundraising
   Programs
      Program 1
      Program 2

Temporarily Restricted:
   Grants
      Grant 1
      Grant 2
   Designated Donations
      Program 1
      Program 2

Permanently Restricted:
   Endowment 1
   Endowment 2

When donors fund a particular program, the funds are restricted until spent on what the donor designated, so they should generally be deposited into a temporarily restricted fund.  Once you’ve spent the money and released the restriction, you should transfer the funds from the temporarily restricted fund to the unrestricted fund.  The easiest way to accomplish this is to set up an Other Expense account called “Transfer to Unrestricted Fund” and an Other Revenue account called “Transfer from Temporarily Restricted Fund”.  Create a journal entry at the end of each month using these two accounts to transfer the funding that’s been released from restrictions.   

There’s no problem if you want to use jobs and I definitely recommend using them for grants, but I wouldn’t use this as a substitution for classes.

You don’t need to re-install QuickBooks to add a new file.  Just go to File > New Company and answer the questions.  However, you might find it easier to just adjust the transactions in your current file.  The easiest way to get a list of all your revenue and expense transactions is to open a Profit & Loss Detail report.  Just click on each transaction and make the changes you want.  However, if you’ve already filed your tax return for 2008 I’d be careful about making any changes.  There’s no problem adding classes and jobs, because they won’t change your basic Profit & Loss, but if you change the revenue or expense account it might.

For fiscal year budgets, you can set up budgets by class at Company > Planning & Budgeting.  For multi-year budgets, you should use estimates at Customers > Create Estimates.  You might need to activate the feature at Edit > Preferences > Jobs & Estimates first.