It is not a good time to rush when creating custom entities in Dynamics CRM. The old adage – “Measure twice, Cut once” couldn’t apply more when working with the initial setup of custom entities. I am sure you have given good consideration to the obvious factors such as the Display Name, the Plural Name and the Database Name (the former two can be changed after the initial setup) prior to clicking on Save.
However, there are a few items that might not be so obvious and are set by default which can put you in an awkward position later as once enabled they cannot be disabled. At least not in a supported method. Those three items are: Notes, Activities and Connections.
You need to read the fine print that once enabled this option cannot be disabled. The best practice is that unless you absolutely positively know that the application will need these features, it is best to uncheck them. At a later date you can always come back in and selectively add them. Just don’t let them go with the default checked status on the basis that no harm will be done. They will be part of the site map and users might utilize them when they shouldn’t.