Understanding SPI Flash better

How much of this regulation is controlled automatically by the flash controller and how much has to be programmed into the firmwar

Espruino can only convert 1s to 0s with a write, and must manually block erase.

You can get an idea of what's available with http://www.espruino.com/Reference#Flash

If the external can handle more write/erase wear, is it being prioritised on the firmware level

On Bangle.js, the external flash is used for everything to be saved. Internal flash isn't use at all.

If I upload a file with same name that already exists to flash, does the file get moved to new cells?

Only if it's different. If it is the same, it is kept.

Espruino basically just works its way around memory 'crossing out' old files and putting new ones in after. It means that it's pretty kind on memory writes since it ends up spreading writes all over the address space.