something like that...
like, say your tree and your pond combined both take up a single palette
you insert these with the rest of your tileset blank on a certain palette, and then switch to a different palette; edit the new palette to have the colors you desire, and then export the tileset with the new colors, ignoring how it messes up the old tiles that you just inserted. add on the tiles that take up a new palette, and then import the new tileset into the palette that was just edited...
so in this example, everything that was not the pond is on a different palette; that is, it was there before. the palette was switched to a new one, the tiles put on the tileset, and the tileset reimported
does that then make sense or no?