3 Step Process.
UperGrafx uses .cdm .img and .sub files. The writing function is not used for the purpose of creating images.
See the instructions here → CD image transfer software?
See the instructions here → PCE - Selecting and Manipulating Disc Images?
Q1, Can I use .ccd image files that I've made with Clone CD? A1. There's no guarantee that they will work correctly, but there is a way to make .cdm files from .ccd files:
Q2. Is there a way to use .cue files? A2. There's no guarantee that they will work, but there is a way to convert them via virtual CD software.
Load the .cue file with virtual CD drive software, select CDManipulator as the virtual drive, and then generate the CD image. It creates .ccd .sub and .img files, .cue files lack most of the disc management data, so the virtual drive completes the missing data via guesswork. So I am not sure if the missing data completed in this way is the same as that of the original game disc.
Q3. I am unable to create a disc image with 99 tracks. A3. This is a bug with CDManipulator.
In order to correct this bug, someone created an alternate version of the software which is available here: dropbox
Q4. My particular optical drive is unable generate the correct data. Other CD image software can't create the correct files. A4. Please use a different drive.
I have received reports that the audio tracks in some games have issues, even when the game data itself runs fine. The drive sends the exact same data to the software, regardless of which software you are using. So in these cases there is no other choice but to use a different drive.
The CD-ROM2 discs have no actual file system, since they were designed to archaic specifications. When the physical discs were being produced, there were many errors present that fell within the error tolerance threshold. Some drives attempt to "correct" these errors, and then send those corrections to the PC, but this can cause issues when playing the image files on the PCE since the data has been altered. These errors on the original discs are unrelated to deterioration or damage. Someone has reported that BD/DVD/CD combo drives might not generate compatible image files. I know this may be troublesome, but please try to use DVD/CD combo drives and use USB-ATAPI adapters. I have used second-hand DVD drives with USB-ATAPI adapters to make compatible disc image files.