There are indeed normally a couple of unused pins at one end of the 'dual in line' pins on a 2.5" drive. You must make sure you get the cable in the correct orientation as the 5V is also fed through the cable (while a 3.5" drive has a seperate 'Molex' connector for power).
Do you have a drive preformatted with AmigaOS or do you have the HD install disks ready ?
Can you see a cradle to fit the hard drive inside the A1200 ?
Good luck :-)