We are staying at Novotel Atlantis hotel. Can we take a subway from the Malgev station in Pudong?

Yes, you first take the maglev in the airport to Longyang Road where you can take the metro line 2 and get off at Century Avenue. Then transfer to take the metro line 4 at the same station and get off at Pudong Avenue. Go out from Exit 3 and walk about 10 minutes later, you will see your hotel.