Use a logical order like you would when you enter an estimate: 1st is the Customer, then the Paper, then the method(Press/Copier), then the Charges: Prep, Bind, Mail.
Assuming that you have already entered your Preferences and filled in the Tables in the Table Editor, this is what I would do:
1. Import and/or Enter your Customers:
Most likely you have your customers in a mailing list or your accounting program. Import them in and then have your CSR’s start entering things like Email addresses (be sure to use the fixed email field = the long one). Enter multiple Contacts etc. This is easy stuff for anyone. This will then allow you to start creating estimates for specific customers.
2. Enter your Top 50 most used Stock Definitions:
Use the ones that come with the system and modify those. No need to start from scratch. Then when you have one that is similar to one you already have just open that one and hit the New button. This will save you trouble of typing repetitive info. Be sure to include a Vendor and the Stock #. This will be important later when you want to increase/change prices. Don’t worry about importing a price book yet.
3. Create your Press Definitions:
Assuming you have already calculated your BHR’s for your company using Ron Teller’s spreadsheet. Keep it simple with 1 definition for each press and then add from there.
Keep it simple at first: Labor Rate, One Average Speed, (Not the advertised fastest speed, but the average speed that your operator actually uses. Then slow it down by 10%.) As you gain more experience, you can create additional definitions for different types and sizes of paper.
4. Create your Copier/Digital Definitions:
You will need the costs from your equipment for at least the last 6 months. I prefer to use the Average Usage per month to calculate the Machine Cost per copy. Enter your Lease, Maintenance, Clicks, Toner, etc. Labor is tricky because most shops don’t have a dedicated employee running a digital machine like our shop does. I don’t have time to type out how to figure that, but I do have a couple Excel Spreadsheets that I use. Email me privately if you are interested.
Now you need to create a Matrix. A matrix is what you are going to charge and you have create that yourself, it is not calculated for you. I usually fill it out from the bottom to the top to be sure I don’t go too low.
Most shops use the Total of Copies method with a Marked Up Stock Cost. This way you don’t have to worry about what kind of paper you’re using.
Here is a link to a previous post about setup:
http://forums.efi.com/showthread.php?t=1629
5. Create your Charge Prices:
Start with Prepress because that is the easiest and is mostly based on time or plates. The ones that ship with the with system are a good start and you just need to modify the Cost and the Price. The cost is important because that is where you enter your Actual Cost with your BHR’s and your Actual Speeds. These are then used to calculate Estimated Times.
Next, enter your Bindery Charges. These can be a little more challenging since they mostly use the Job Aware method which means that you have to choose what factors PS must use to calculate the price: Ordered vs. Press Qty; Colors vs. Sides; Sheets vs. Sigs; x Up or / Up; There are some great examples that ship with the system.
Keep in mind that you can also create Rate Lists or Price Lists based on Qty so you can have a Sliding Scale.
6. Start Using PrintSmith:
The only way to learn how the things you have setup work is to test it by entering the current estimates and invoices that you currently have. I agree with Jeff that it is better to use Line Item Discounts/Adjustments to get the prices you want instead of Overrides. I got bit today by an Override but it was in our favor, so the customer didn’t mind when I told them their price was lower. You are going to have a lot of Legacy Pricing issues at first until you tweak your system. “We charged $500 last year but PrintSmith says the price should be $600.”
Don’t worry about messing anything up. Before you Go Live, you can get rid of any of the Invoices or Billing that you only did for testing.
Lastly, you will never be “done” setting up. Welcome to Kaizen, what the Japanese call Continuous Improvement.
Good luck! 
Woodruff Consulting 