Generally if the game wants you to draw from the Legacy deck, it'll say "draw and keep the next card in the Legacy deck." If it's just telling you to draw and keep "the top item card," they mean from the Item draw pile.
If the next card in the Legacy deck is an item, it'd probably get shuffled into the item pile anyway so if you drew and kept that one instead, it wouldn't necessarily affect much, other than giving you a surer chance of having something you could heirloom instead of ending up with an already-heirloomed item.
If the next card in the Legacy deck is an item, it'd probably get shuffled into the item pile anyway so if you drew and kept that one instead, it wouldn't necessarily affect much, other than giving you a surer chance of having something you could heirloom instead of ending up with an already-heirloomed item.