The format which all Amiga CD file systems can read is ISO9660 level 2 with Amiga extensions. It's not very likely that you find a Windows program which can create this.
What comes next is ISO9660 level 2 with Rockridge extensions.
If your program does not allow to add options to the ISO format, you will get pure ISO9660 level 2 which means all file names are translated to upper case, truncated to 32 characters and each file name may contain only one dot.
However, if you use a CD file system like CacheCDFS, AsimCDFS or AllegroCDFS, you can as well use Joliet which is standard on Windows. These file systems can read Joliet. Other file systems might show only upper case files truncated to 8 characters + 3 characters extension.
If I were you I would use WinUAE, install a nice little AmigaOS and use MakeCD to write the CD. Then I'd be sure that it can be read by every Amiga.
Bye,
Thomas
