The stepRocker has six inputs for stop switches (L1, R1, L2, R2, L3, R3) which are inputs only and on the 2x7 pin connector there are some additional I/O lines. With the actual firmware (at least V1.01, better V1.02) five pins on that connector can be used as general purpose outputs and four other pins can be used as general purpose outputs (one of them also as an analogue input).
Please see chapter 5.5.14 (SIO command) and chapter 5.5.15 (GIO command). There you will find which pins can be used as outputs and which as inputs and what commands to use. You do not need to change any main settings.