Try to complete the majority of the setup and configuration on your Custom Object before creating your reporting. Frequently you will need to create custom Report Types to facilitate all the reporting requirements for your Custom Objects. The number of custom Report Types you might need to create will be dictated by the number of look-up fields and master-detail relationships in your Custom Object (i.e. how many ways does your new object “join” to other objects in Salesforce). Custom Report Types are available via Setup > App Setup > Create > Report Types.
Why I stress leaving reporting for last is that if you create your custom Report Types early in the process, and then you create additional fields for your Custom Object later, you will have to go back and add those fields to be available to the custom Report Type otherwise they will not be available (you won’t see them!) in the report wizard.
This catches a lot of Administrators off guard. They go back and make an update to the custom object and then they go to make a report or update a report to include the fields they just created and they do not appear in the reporting wizard. The natural reaction is to check things like fields level security on the profile (which can also prevent a User from seeing a field in the report wizard), but in fact the issue is that the custom Report Types must also be updated if the new field(s) were created after the custom Record Type was created.