What do you mean by basic links? I write 100% of my links in markdown and export them just fine.
As for showing the connection between notes, I don’t rely on the ziplink method for connecting inline text to another note; I find it very limited. Rather, I’ve written an action code that links my notes by pulling values from attributes or I’ll use the link parking lot. I can then use the Links Pane to navigate these notes, leverage hyperbolic view, etc. This is the more scalable route to go.
I’ve/we’ve made several videos on linking: Mastering Tinderbox: Training Videos (Complete List). If you show up at one of the weekly meetup we can also go through it again live. Or, if you can’t make it please outline the project you’re working on and I can make something up.