All you have to do is change one thing in the trainerbattle command:
trainerbattle 0x[battle type] 0x[Trainer ID] 0x0 [pointers to messages]
That's the part in bold. Instead of that byte being 0x0 as it usually is, change it to 0x100, 0x200, 0x300, etc... depending on the slot of the palette you want to use in your table. So 0x100 would be the first palette...and so on.
If you have put 800000 in place of the Fs, then the ASM will think that your table is at 0x800000. So starting at that offset, put the pointers to your palettes.