Tip: Layer 3 backgrounds and tides disappear when you hit a message box, so plan your level around that. For example, you can add a sublevel without layer 3 at the start/midpoint, and include your message there.
How do I make the Hammer (the Amazing Flyin' Hammer Bro. hammer, not the hammer from the castle cutscene) use palette 9 instead of B. It seems to not be editable in Tweaker.
Open the CFG Editor (which comes with Sprite Tool), click on "Open", and look for the .CFG file of your sprite. There you will see some strange things, but you only need to change the Palette box to the palette you want your sprite to use.