Espruino on your watch!

You might be better creating a new jswrap_... C file and then using the _init callback on it to run stuff at boot. Or you can use the Espruino CLI to make a HEX file for .boot0 which you can then merge with the hex file?

Also what is best way to store relatively big data like bitmaps, fonts so it is not copied to RAM but could be read directly from flash as constants?

You could add them as files in Storage, or could put them inside a function written in a module (or just code file) in Storage. That way they stay in flash, but just get loaded into RAM when used.