There is no relationship.
An App42 application that you create in AppHQ is a sandbox environment for your application's backend on our cloud. Each App42 application sandbox is distinguished by its apikey and secretkey.
The project that you create in Eclipse will contain the client side code.
To make your client-side application talk to the backend - you will need to pass the api-key and secret-key of the backend application you created from apphq.