I haven't used coverXP for a while but this worked on version 1.52.
Install the program as normal, then, export the reg info from here
CODE
HKEY_CURRENT_USER\Software\coverXP
Copy the coverXP install directory from Program Files and incorporate it into your unattended cd, then create a sfx with WinRAR to copy the files back to Program Files and import the reg file.
Another way if you use the OEM preinstall option is to create a folder called $Progs in the $OEM$ folder, put the coverxp folder in it and then add the reg info to your tweaks reg file, this will get copied during windows setup.