tl;dr: Any time the queen is wearing the black dress with the feathered headdress or the red-and-black battle dress, it's Sabé/Keira.
Note that the following is written from an in-universe perspective, but the answer doesn't change for an out-of-universe perspective: there are no scenes where Keira plays Padmé or Natalie plays Sabé. (There are promotional materials that mix them up, but that's a different matter.)
That's Sabé on the left, Padmé second from right. Rabé is behind Sabé, and the other two are Yané and Saché, but I can never tell those two apart.
Left to right: Rabé, Eirtaé, Anakin, soldier, Sabé, Padmé.
The first time we see Sabé (in any dress) is when the "queen" and her handmaidens are escorted down that grand staircase. All through that scene, the subsequent rescue, any scenes on the ship on the trip to Coruscant (via Tatooine), and the arrival on Coruscant, it's Sabé posing as the queen.
On Coruscant, we briefly see Sabé in the "Anakin can't count" scene1, in the scene in Palpatine's quarters after the Senate debate, and when they re-board the ship, but in all three scenes, she's dressed as a handmaiden (black senate cloak, red cloak, and flame dress, respectively), not the queen.
We next see Sabé, dressed as the queen in the red and black battle dress, back on Naboo. All through the battle planning and the appeal to the Gungans, it's Sabé acting as the queen. Even after the ruse is revealed, Sabé stays in the queen's getup, which comes in handy when they're battling in the palace and she's captured.
In all subsequent appearances (greeting Palpatine in the yellow throne room dress, at Qui-Gon's funeral in a dark cloak, and at the end parade in the green dress), the queen is really the queen, and Sabé is a handmaiden.
(All credit to The Royal Handmaiden Society for the images and the refresher on who's where when.)
1 It's the scene where Rabé tells Anakin that Padmé isn't there, yet clearly all three handmaidens who came on the trip are in the room.