First you have to define the accounting structure, Cyclos comes with default transactions and accounts that may or may not be useful for your business model.
First of all, probably you will want to remove or inactivate the accounts and transactions you will not use and leave the ones you want to use by giving them meaningful names and descriptions. This is by far the hardest task you will have to commit. If you need help here, we can start a project to consult you. Please contact our helpdesk.
Then you have to define the group structure, if you need to use other structure than the default one.
There are system and other settings that you have to fine tune before launching your project. More info:
http://www.cyclos.org/wiki/index.php?title=Business_rules