The green shape is the timeline. Red lines represent specific moments in time (I chose a handful for purposes of illustration.) Blue represents Harry and Hermione.
Moment 1: Harry and Hermione A are down at Hagrid's hut with Ron.
Moment 2: Someone hits Harry-A in the back of the head with a stone. H&H-A leave Hagrid's as the executioner prepares to kill Buckbeak.
Moment 3: H&H-A are saved from being eaten as Werewolf!Lupin runs off to investigate a howl.
Moment 4: Harry-A and Sirius are saved from the Dementors by someone casting a Patronus across the lake.
Moment 5: H&H-A use the Time Turner to go backward in time to Moment 1.
Now we start over. Harry & Hermione-A become Harry & Hermione-B. Both sets are in the same timeline and can potentially see, hear, and interact with one another, but H&H-B are of course hiding from H&H-A.
Moment 1: H&H-B arrive and lurk in waiting until...
Moment 2: Hermione-B throws a rock at Harry-A; H&H-B watch H&H-A leave the hut; then the B's rescue Buckbeak.
Moment 3: Hermione-B howls, luring Werewolf!Lupin away from H&H-A.
Moment 4: Harry-B casts the Patronus, saving Harry-A and Sirius.
Moment 5: H&H-B return to the Hospital Wing, just in time to see H&H-A leave via the Time Turner.