You can still apply gecko codes on an ISO via the conventional method (Place codes on GCT, GCT in SD, Ocarina ON in USB Loader). By the way, MKWii.com has its own GCT creator (credits to WhatIsLoaf) - https://mkwii.com/gct/
If you instead want the GCT "edited" onto the ISO itself, you need Wiimm's SZS tools. Once installed, you need to extract the ISO, patch the main.dol, then rebuild it. Command to edit the main.dol is this...
wstrt patch main.dol --add-section nameofgct.gct
If that's the method you want, I have a whole subforum explain Wiimm's tools and how to use them - https://mariokartwii.com/forumdisplay.php?fid=17
Finally, (I HIGHLY doubt this is what you want), you can literally hex edit codes onto the ISO. https://mariokartwii.com/showthread.php?tid=419
If you instead want the GCT "edited" onto the ISO itself, you need Wiimm's SZS tools. Once installed, you need to extract the ISO, patch the main.dol, then rebuild it. Command to edit the main.dol is this...
wstrt patch main.dol --add-section nameofgct.gct
If that's the method you want, I have a whole subforum explain Wiimm's tools and how to use them - https://mariokartwii.com/forumdisplay.php?fid=17
Finally, (I HIGHLY doubt this is what you want), you can literally hex edit codes onto the ISO. https://mariokartwii.com/showthread.php?tid=419