Not sure what the brown marks are unless as said they are spots of Tar etc?
Unless your water is really dirty that your washing it with, making it look brown and streaky? The 2 bucket method should eiminate this though.
I clean the windscreen/windows regular with Autosmart Glass Clear, but if you protect it with something like G Techniq's range, then it will repel water at speeds above 30MPH, and help keep it clean.
I just use Poorboys Natural Look Dressing for interior plastics etc, and give the nav screen a wipe over with the same cloth once its dried up a bit. Always works wonders!
Leather wipes are ok, but the Gliptone kit is good also, but thats more if the leather is dirty and needs cleaning, then protecting.