Thinking of creating a drone that would use multiple shields stacked together, with a protoboard on top. When connected to other various shields, would I still be able to use every external connection labeled on the protoboard? Cannot find this on the website or anywhere online, please help.

Everything shares the same 20 I/O that are available on the proto board- you'll need to check each schematic(on the product page or our github) and see which pins are still available at the proto board, as our compatibility matrix at https://www.tiny-circuits.com/index.php/tiny-duino/tinyshield-compat/ only covers whether or not our shields are compatible.