Raphael, the Muscle

The damage is dealt by the same source as the original source of damage. The doubled damage isn't dealt by Raphael unless he was the original source of damage.

Once the game begins, your two commanders are tracked separately. If you cast one, you won't have to pay an additional {2} the first time you cast the other. A player loses the game after having been dealt 21 damage from any one of them, not from both of them combined.

If other effects modify how much damage a creature you control with counters on it would deal—by preventing some of it, for example—the player being dealt damage or the controller of the permanent being dealt damage chooses the order in which any such effects (including Raphael's) apply. If all of the damage is prevented, Raphael's effect no longer applies.

If your Commander deck has two commanders, you can only include cards whose own color identities are also found in your commanders' combined color identities. If Donatello, the Brains and Splinter, the Mentor are your commanders, your deck may contain cards with blue and/or black in their color identity, but not cards with red, green, or white. (If Leonardo, the Balance is one of your commanders, your deck may contain cards with any color or combination of colors in their color identity, regardless of who your other commander is.)

If damage dealt by a creature you control with counters on it is being divided or assigned among multiple permanents and/or players, that damage is divided or assigned before doubling. For example, if you attack with a 5/5 creature with trample and it's blocked by a 2/2 creature, you can assign 2 damage to the blocker and 3 damage to the defending player. Those amounts are then doubled to 4 and 6, respectively.

To have two commanders, both must have appropriate partner abilities as the game begins. Losing the ability during the game doesn't cause either to cease to be your commander.