There are no more settings required for ISAPI deployment except those required for IIS.
Well, when ıt comes to IIS there are security issues which prevents program from accessing all resources. It restricts you to IUSR and IUSR_IWAM accounts' privileges. If you need to access a folder or file for read/write access then you must grant it to IUSR account.
Can you send a screen shot of garbled web browser screen?