Just like in a real fight, keeping your guard up requires presence of mind. After being hit, you stop blocking unless you're holding a back directional input or the string jails. Some powerful moves can break neutral guard even on block, such as Heihachi's UF3-4. This means if you block the first hit but aren't holding back for the second, the second will hit you. This can cause you to get hit while backdashing, since tapping back-back isn't holding back.
Neutral guard also applies to crouching. Holding down will block lows, but not all of them. Rule of thumb: if you intend on blocking, hold back, whether standing or crouching.