• Set up the Chart of Accounts in accordance to the 990. The most common error  I have seen is a Chart of Accounts that is too large.  Keep it small and use the Customers and Classes for your detail.
• Adding an account called “Ask the Accountant” enables the user to add a transaction right away  and then when the accountant is available all transactions that the user was unsure of are with are posted in one spot.
   
• Use Customers as Donors and/or Grants – Identify your funding source (Use Jobs for each year or phases of the Grants)
   
• Use Classes as Programs and Activities that you provide. There are three main categories – program, management, and fundraising. By starting with these main categories reports can be run when it is time to fill out your 990. Add your activities within each of these functions as subclasses. 
   
• Use Items as – What you sell or services you provide (Memberships, dues, fees, tuition, donations, merchandise).
   
• Use Customer Type as a way to make it easier to filter your Customer and Jobs.
• Job (Grant) Types: Time restricted grants, use restricted grants, permanently restricted grants
• Customer (Donor) Types: regular, grantor, large, bronze, etc.

Additional Setting Tips
 
Under preferences I recommend these settings:

• Show the Lowest sub account only: this setting allows you to more effectively use sub accounts by hiding the name of the parent account. (This feature can only be used if you have account numbers assigned to your accounts.)
   
• Required accounts: this forces the user to code every transaction to an account.
   
• Use class tracking: this setting enables class (activity) tracking in the company file.
   
• Prompt to assign classes: this setting activates a message reminding you that the Class field has not been used in a transaction. (This is very important when using classes.)
   
• Use audit trail: this setting is important for providing back-up for transactions.