Maybe I should start by asking: can the pins that I've marked on the picture be accessed directly? The individual pins don't seem to be marked, are they only meant for programming the chip? If not, how do I know what they're called when writing Verilog code?
If it still actual, you can use one PMOD for direct access to programmable logic. This is the down 12 pins that you've marked. The Pmod connector is a2x6 right-angle, 100-mil female connector that mateswith standard 2x6 pin headers available from a variety of catalog distributors. The12-pin Pmod connector providestwo VCC signals (pins 6 and 12), two Ground signals (pins 5 and 11), and eight logic signals. VCC and Ground pins can deliver up to 1A of current.Jumper JP12 selects the Pmod Vcc voltage(3.3V or 2.5V)in addition to selecting the VHDC voltage. Pmod data signals are not matched pairs, and they are routed using best-available tracks without impedance control or delay matching. Pmod Pinout
JA1: T3
JA2: R3
JA3: P6
JA4: N5
JA7: V9
JA8: T9
JA9: V4
JA10: T4