These are general questions about the game that don't really fit anywhere else.
What color is used as transparent in splash.bm2?
255, 0, 255, which is a sort of purple.
What program should I use to open .bm2 and .wa2 files with?
You can just rename these extensions to .bmp and .wav respectively. Then they should open with your favourite viewer/editor automatically.
I try to download a map but I am just shown the tileset in my browser
You need to right click and save the link to disk. The beginning of the data inside a map is a bitmap.
How do I change the F1 help box?