To answer your question, you must redraw the entire taxiway and runway network and replace the default one. There is no way to have two networks interact with each other.
Personally, I use Airport Design Editor (ADE) to convert airports into a project for me, and then work on them in the sim Devmode Scenery Editor. I do that because I like to edit the airport in context in the sim rather than in another interface, and I’d rather not switch back and forth between ADE or have to learn yet another interface. In the past, it also was a better idea to edit in either one or the other and not both, I don’t know if that’s been improved by now or not.
Granted, if you’re ONLY editing the taxiways, then maybe that’s easier in ADE, I don’t know, I haven’t tried. But it seems to me in sim is the best as you can see how the changes fit in the context of everything, which you can’t see in ADE, as it doesn’t open up a “sim view”.