Where does Hexpion go being under the Backup Copy?
The active player decides which order the destroyed abilities resolve in.
Because the creature has two separate destroyed abilities, they both trigger at the same time.
If Backup Copy resolves first, you'll (probably) have Hexpion in archive:

Backup Copy moves Hexpion to the top of the deck.
Hexpion's ability can't track it anymore (see the rule from page 13 below), so you just do the second part of it (archive the top card of the deck). As long as nothing weird has happened, that card just so happens to be Hexpion!

If Hexpion resolves first, Backup Copy does nothing:

Hexpion puts itself and the top card of the deck into the archive.
Backup Copy resolves, but can't interact with Hexpion because it's been moved to a hidden zone.

From the rules, page 9:

ACTIVE PLAYER
The active player is the player taking the current turn. The active player makes all necessary decisions for all card abilities or timing conflicts that need to resolve during their turn.

Page 13:

When a card moves from an in–play zone to an out-of-play zone in which the identities of cards are hidden from the opponent (such as a player’s hand, deck, or archives), any pending effects that are currently or about to interact with that card no longer do so, unless a card effect explicitly states that it interacts with that zone.