Much like adding new roms for the cart system, you'll need to add an entry to neocd.xml in the hash folder; this is what I have (though it might be out of date) in there:

<software name="fmstudio">
	<description>FM Studio</description>
	<year>2016</year>
	<publisher>freemco</publisher>
	<part name="cdrom" interface="neocd_cdrom">
		<diskarea name="cdrom">
			<disk name="fmstudio" sha1="4c8ee173d4920718b0279f74e711131ff6ef6c3e"/>
		</diskarea>
	</part>
</software>