@crossingthethreshold its a good question. I am still playing with this. Needless to say if the answer was simple I would have had the answer instantly. I'm honestly leaning towards iAWriter, but it all has to go through iCloud for that to work.
@kaa While iA Writer is still my go to writing app, I use 1Writer as my iOS The Archive app. It supports tags, multiple folder directories and supports Markdown . Most of my note taking takes place on my laptop, but when I need an ios app, 1Writer is fulfilling that need.