Make sure your Mdnotes settings are set to ‘Single file’ and then use the ‘Create full export note’ option. Try it out with the standard templates, but you may need to tweak them to get it to render how you want.
In a nutshell, the full export makes one .md file that first takes the contents of the template ‘Mdnotes Default Template.md’ (this is where metadata, links, abstracts, etc can be brought in from) then adds your notes and extractions using the ‘Zotero note template’ (notes and annotations). It iterates the note template over each of your notes, so if you have a standalone note and extracted highlights, you’ll get it twice. This is fine, depending on how you have the content/templates set up.
Configuring templates and output is a pretty deep rabbit hole that I keep falling jumping down. You’ll probably want to review this great writeup (maybe minus the dataview bits unless you want them too - I don’t use much dataview tbh) and really read over the Mdnotes docs (first link).
Good luck. I’ve been happy with this approach so far.
edit after re-reading your post - It looks like you just need help setting up the templates. Start with the first link I gave and ask questions as you come across them.