I have the MM6501 installed in the front doors of my 2002 WRX. I didn't use spacers and just drilled them straight to the doors. They are pretty slim due to the neodymium magnets but the windows do hit them when you roll them down. I would say the window sticks up out of the door about 1 inch before they hit the magnets.
If you don't want your windows to hit, you should get spacers. I got a set of spacers from PVC Speaker Adapters - CNC Machined - In Stock or Custom Made
that I haven't used if you would like to buy them.
As far as the tweeter goes, I mounted it in my stock location. No additional hardware needed.
I'm also currently installing a set of MM521 in the rear doors, but I will need to cut out some of the door to get the speaker to fit.