How do i need to set up to make sure my putter is on my target line every time?

Do the old "railroad tracks" drill. Set up two clubs/shafts/brooms side-by-side. One "track" is for the ball, the other is for your feet. Point the shafts in the direction of the intended line- this drill works best if done on a flat green- and set up to the ball. Where's your shoulders pointing? Where's the putter's face pointing? Once you get the feel, you can remove the sticks and make some putts. If you're still off, go back and see what's happening. If you're absolutely sure your alignment is correct, you may be having trouble with the stroke.