The TO3000 workflow is quite easy:

1. Go to the "Client" window and click the "New Client" button.
2. Input the client name and choose the currency.
3. Add any required information about the client like the address, contact info, invoicing policy, payment terms, etc.
4. In the "Contacts" tab you can add the client's contacts.
5. In the Prices tab you can add the unique price list for this client.
6. When you receive a job, you can add it by clicking the "New" button on the "Client Jobs" tab.
7. When the job is completed, you can go to this job and check the "Completed" checkbox.
8. When you need to issue an invoice for the completed job, just switch to the "Invoices" tab, click the "New" button and add that job to the invoice. Then you will be able to specify discounts, taxes for this invoice and save it as a .DOC, .RTF or .PDF file.
9. When you receive a payment, you can track it on the Payments tab, linking the payment with the appropriate invoice.

Please note that the above operations are specified for the Without Projects Mode which can be selected in the "Advanced settings > Workflow Mode" window.

Also, it is recommended to watch our webinar about TO3000 on ProZ. It is available at: 
http://www.proz.com/videos/Free webinar week videos/3032

Note: the webinar uses an older version of TO3000, but the basic workflow structure is the same in the current version.