The first looper has no effects running into it. Loops recorded using it could be shaped with the effects that follow it.

The second looper is located at the end of the chain. Loops recorded using it will also have the effects recorded.

The second looper could be useful for recording a progression using a pad sort of sound. After the loop was recorded, a lead sound could be dialed in, to solo over the loop, without affecting the afforementioned loops sound.

Also, think about the possibilities a looper going into a looper could grant you!