Enter them at the password screen:

Charge Man defeated with beat power
Red:B1,F3,F5; Blue:C1,D4,F6

Crystal Man defeated with beat power
Red:D2,D3,F5; Blue:C1,D4,F6

Gravity Man defeated with beat power
Red:B1,D3,C6; Blue:C1,D4,F6

Gyro Man defeated with beat power
Red:B1,A4,F5; Blue:C1,D4,F6

Napalm Man defeated with beat power
Red:E2,D3,F5; Blue:C1,D4,F6

Proto Man's Castle with beat power
Red:C1,D4,F6; Blue:F1,B4,D6

Star Man defeated with beat power
Red:B1,F4,F5; Blue:C1,D4,F6

Start game with beat power
Red:B1,D3,F5; Blue:C1,D4,F6

Stone Man defeated with beat power
Red:B1,D3,B5; Blue:C1,D4,F6

Wave Man defeated with beat power
Red:B1,D3,B6; Blue:C1,D4,F6

Charge Man defeated
Red:C1,D4,F6; Blue:B4,D6,F1

Crystal Man defeated
Red:A5,D2,E3; Blue:B1,B3,E5

Gravity Man defeated
Red:A5,B1,F4; Blue:C4,E5,F1

Gyro Man defeated
Red:A5,B1,E3; Blue:B3,E5,F1

Napalm Man defeated
Red:A5,C1,E3; Blue:B3,E2,E5

Star Man defeated
Red:B1,B6,F4; Blue:C4,E6,F1

Stone Man defeated
Red:C1,E3,F6; Blue:B3,D6,E2

Wave Man defeated
Red:B1,B6,D3; Blue:B3,E6,F1

Dr. Wily's lair
Red:C1,D4,F6; Blue:B4,D6,F1