I have spanish iso set in preferences, but half the keys are not mapped properly. The square brackets, tilda and various other keys are wrong. Is there anyway to get correct mappings?

Are you using a Apple keyboard or a regular PC keyboard? I am asking this because Apple uses a slightly different mapping.

Apple Keyboard (german layout):
@ = alt-l
[ = alt-5
] = alt-6
~ = alt-n
...

It's a pc keyboard. Now I played around with it a bit, I see the windows key in combination with `+ gives the square brackets. Normally you would use the alt-gr key

Thats weird indeed. On my old Logitech G15 Keyboard the Windows key served as Command Key (Apple Key), while yours seem to act like an Alt button.

Get Ukelele.

If using a Logitech PC keyboard, alternatively you can install the Logitech Control Center software for OSX, which has a setting somewhere in its control panel to tell it that you're using a PC keyboard.