In the divergent timeline of the J. J. Abrams films, where were
Khan and his Botany Bay "family"
before Admiral Marcus woke him up and enlisted his services?
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An unspecified location in deep space:
Khan: For centuries we slept, hoping when we awoke things would be different. But as a result of the destruction of Vulcan, your Starfleet began to aggressively search distant quadrants of space; my ship was found adrift
According to "Space Seed", the Botany Bay (Khan's cryoship) was launched in the 1990's, well before the timelines diverged, so they would have been on the same course in both adaptations.
According to Memory Alpha, "Space Seed" takes place in the year 2267, and Star Trek Into Darkness in 2259. Given how close in time the two adaptations take place, it's likely that the Botany Bay was in more or less the same part of deep space in both adaptations.
There're two other pieces of information: in "Space Seed", Kirk order the Botany Bay be towed to Starbase 12. TNG production art2 established that Starbase 12 is in Sector 25712, which also contains the pleasure planet Risa.
The second piece of information is that, also in "Space Seed", Khan and his crew are deposited by the Enterprise on the planet Ceti Alpha V. The events of the episode occur over a roughly 34 hour period1, so presumably the ship was about 34 hours journey from Ceti Alpha V, in the direction of Starbase 12, at unknown (but presumably high) warp. For whatever that's worth.
1 According to this answer, and using the TOS stardate scheme; in Kirk's opening Captain's Log he gives the stardate as 3141.9. After reclaiming his ship, he has another Captain's log where he gives the stardate as 3143.3. Since each 0.1 of a stardate corresponds to 1/10th of a day (according to the linked answer), this gives 33.6 hours
2 As Xantec points out in comments, I've assumed that the Starbase 12 referenced in TNG (set in ~2366) is the same as the one mentioned in "Space Seed" (set a century earlier). While this may not be a reasonable thing to assume, it's the only reference I could find