Yes it is quite easy. In config tool select for example E2 (third extruder) as motor. That will result in something like
#define EXT2_STEP_PIN ORIG_E2_STEP_PIN
#define EXT2_DIR_PIN ORIG_E2_DIR_PIN
#define EXT2_ENABLE_PIN ORIG_E2_ENABLE_PIN
now these variables are undefined, so in manual additions in config tool you add
#undef EXT2_STEP_PIN
#undef EXT2_DIR_PIN
#undef EXT2_ENABLE_PIN
#define EXT2_STEP_PIN 10
#define EXT2_DIR_PIN 11
#define EXT2_ENABLE_PIN 12
with 10-12 replaced by correct pin number. That's all required.