Bingowings said:

I was thinking of storyboarding a sequence where Amidala's ship double's as a sub so she can meet Boss Nass at the Gungan City instead of the 'sacred place'.

I was thinking the same. Only, after her ship is landing maybe you can just cut to Qui Gonn, Obi and Jar Jar approaching and going into the water. Then when they meet Boss Nass, a hologram of the Queen appears right after Boss Nass says that he don't like the Naboo. (We need a scene where the good guys explain to Boss Nass what happens on the surface before the Queen asks them to help her, I think.)

Then:

- Whossa this?

- I am Queen Amidala (etc...)

Plus I think a hologram of the Queen would be much easier to do than to replace the whole set behind all the characters. (Some set behind Boss Nass would need some replacement though)