

Q1: Can I return just 1 of the specified cards to the bottom of the deck for the conditions of this card's Opponent's Turn effect?
No, you can't. A "by" condition can't be met if only some of the required actions are performed. The conditions for this Opponent's Turn effect require you to return the specified number of cards to the bottom of the deck.
Lv.6 Amphimon P-089 P Mega | Data | Cyborg [When Digivolving] You may trash up to 3 blue cards from your hand. For each card trashed by this effect, you may choose 1 of your opponent's Digimon or Tamers and trash it. Then, 1 of your opponent's Digimon or Tamers without cards under it can't suspend until the end of your opponent's turn. [Opponent's Turn] [Once Per Turn] When an opponent's Digimon attacks, end that attack by returning 3 cards with [Jellymon] in their text from your trash to the bottom of your deck. ---
Lv.6 Amphimon P-089 P Mega | Data | Cyborg [When Digivolving] You may trash up to 3 blue cards from your hand. For each card trashed by this effect, you may choose 1 of your opponent's Digimon/Tamers and trash it. Then, 1 of your opponent's Digimon/Tamers without cards under it can't suspend until the end of your opponent's turn. [Opponent's Turn] [Once Per Turn] When an opponent's Digimon attacks, end that attack by returning 3 cards with [Jellymon] in their text from your trash to the bottom of your deck. --- -
Lv.6 Amphimon P-089 P Mega | Data | Cyborg [When Digivolving] You may trash up to 3 blue cards from your hand. For each card trashed by this effect, you may trash 1 card under 1 of your opponent's Digimon or Tamers. Then, 1 of your opponent's Digimon or Tamers without cards under it can't suspend until the end of your opponent's turn. [Opponent's Turn] [Once Per Turn] When an opponent's Digimon attacks, end the attack by returning 3 cards with [Jellymon] in their text from your trash to the bottom of your deck.
Lv.6 アンフィモン P-089 P 究極体 | データ種 | サイボーグ型 【進化時】自分の手札の青のカードを3枚まで破棄できる。この効果で破棄した1枚ごとに、相手のデジモンかテイマーの下から選んで1枚破棄できる。その後、次の相手のターン終了まで、下にカードが無い相手のデジモンかテイマー1体はレストできない。 【相手のターン】[ターンに1回]相手のデジモンがアタックしたとき、自分のトラッシュから、「ジェリーモン」の記述があるカード3枚をデッキの下に戻すことで、そのアタックを終了させる。 ---