Research at the county-level: Macro or Micro? Is research at the county-level considered applied micro or applied micro? 

The standard undergrad definitions ("micro" = "individual", "macro" = "nation") are of no help with units of measurement that lie in between.

Any help is appreciated.
I would consider county-level research macroeconomics.

Microeconomics focuses on individuals and firms acting as decision makers. I think, looking at county-level aggregates, you are too high level to look at decision makers.