Youll know a monster belongs in the Extra Deck if it has Fusion, Synchro, Xyz or Link in bold on its card text
Something important to note here is that these arent necessarily the best decks overall in Yu-Gi-Oh itself, and a lot of decks in Master Duel actually arent very good in the main TCG game but ARE good in the game thanks to a completely different ban list
The app only allows users to create multiple decks within the same game version and does not support mixing decks from different game versions

cards All Paleozoic cards All Phantasm Spiral cards, including Pacifis, the Phantasm City All Plunder Patrol cards All Prank-Kids cards All Primite cards All PSY-Frame cards All Purrely cards All Qli, Qliphort cards All Ragnaraika cards All Regenesis cards All Rescue-ACE cards All Rikka cards All Ritual Beast cards All Runick cards All Ryu-Ge cards All Ryzeal cards All S-Force cards All Scareclaw cards All Shaddoll cards All Shiranui All Sinful Spoil cards All Six Samurai cards and Shien cards, except Hand of the Six Samurai, Tenkabito Shien and Shiens Spy All Sky Striker cards All Skull Servant/Wight cards All Snake-Eye cards All Solfarchord cards All Spright cards All Springans cards All SPYRAL cards, including Charming Resort Staff, and SPYGAL Misty All Starry cards, except Starry Dragons Cycle All Subterror cards Super Quantum Black Layer, Super Quantal Fairy Zetan, and Layer 19 Sudden Incursion