umm might be a silly question but i took my caliper off and need to refix it. Its one that you fit by applying the brake and tighten the bolts. I’m guessing its better to refix it with new pads in to get the correct position?

Yes,and you’ll be very lucky to get it right just pulling and tightening, five minutes extra spent making sure both pads hit the disc dead square and at the same time will pay off with better feel, power and pad life.