With the earlier reveal now edited out, we've only seen Natalie Portman giving orders before the raid - it's clear at this point that this is the queen, but not clear that she is wearing one of Padme's outfits. She does not change costume after this point. The decoy doesn't appear (iirc) until the scene in the throne room, and a throwaway "my decoy!" as the doors open is enough IMO to confuse Gunray and enlighten the audience.
The alternative would be to splice some Neeson dialogue into an earlier scene (because Qui-Gonn has quite clearly sussed that Padme===Amidala already) so that he addresses Padme as "Queen". I can't think of a suitable place for this to occur, though.
Someone mentioned earlier that the whole bongo scene can be removed, and I like this idea. However, filmically, I think the audience needs to see the Gungan city so that they have some empathy with the Gungans (and have met them in a quasi-intelligent capacity) before the battle. It also allows Jar Jar to come out of the swamp later and comment something like "a massacre... they're all dead!", just before the raid briefing scene.