Ah. That doesn't sound too bad!
Normally during image deployment, CloneDeploy changes the computer name in the Windows registry if no answer file is found in the image. However, that functionality doesn't seem to be working at the moment. CloneDeploy most likely needs a small update to fix that functionality. As far as the answer file goes, once sysprep is run, that is when the answer file gets executed. As CloneDeploy is not currently changing the Windows registry, you will have to make an answer file for auto renaming. You will also have to add sysprep tags under Sysprep in the image profile for any changes that you want CloneDeploy to make to your image. Overall, it's generally best practice to upload pre-sysprepped and sysprepped images.
Usually, what you would do first is prepare a Windows image in audit mode before running sysprep. While in audit mode, you would install any drivers, software applications, scripts, and unattend.xml answer files. Then, you would upload the pre-sysprepped image with CloneDeploy. After that, you would run sysprep on the Windows image. Once sysprep has been run on the Windows image, the computer shuts itself down. This is when CloneDeploy steps in with the sysprep tags. Also, this is when you would upload a second image with CloneDeploy. This second image is the sysprepped image. The first pre-sysprepped image will be used for updating the image later on down the line. Next, the answer file gets executed after boot. However, before any execution of the answer file takes place, CloneDeploy changes your defined sysprep tags that were under Sysprep in the image profile. After CloneDeploy is done changing the syprep tags, the Windows image executes the answer file and boots up like normal (e.g. into OOBE mode or the desktop).
Does that help at all?