You only need progmem once, prog_int16_t re-implements it, just use int16_t
int16_t accAxisX[][rowSize] PROGMEM = {{ 1, 2 },{ 1, 2 }};
Your data can only be set in the initializer list ( bit above in {} brackets ). Not at runtime.
If your data can be computed at compile time, you can fill the array then. Otherwise you will need to use a standard array.