so, im a little nervous, but who wouldnt be? its my first time doing something like this.. but i know you just tac around to not warp the peice etc. but my question is..how can i know where to cut? the ones i have, have the flanged end up on top. but how can i know where to cut because of this?

http://mustangsunlimited.com/itemdy00.asp?T1=88100+01if you look up top, you can see what im talking about

 

Measure the new piece from the bottom of the panel up to the step in the patch. Do not measure the step when you do this. Then measure the quarter up from the bottom to achieve this measurement. If the patch was 13" high to the step measure up 12" on the quarter for making your cut. Leaving the extra 1" will allow for error. Then start fitting the patch and trimming the quarter untill you achieve the proper fittment. Make sure to leave the step on the patch. Once you have it where you want it clean both pieces for welding. Refit the patch and screw in the patch with some self tappers. Dont forget to put holes in the patch for plug welding around the wheelhouse and the trunk drop off and where it wraps around the back.Slowly tack the seam together on the face of the quarter jumping from one end to the other so you dont overheat the panel. I throw a handful of tacks on let cool for a bit then keep doing this over until I have a solid weld.

 

?? all i was gunna do was trace around the top of the panel to the car, then measure the distance from the top to the lip and then tac weld

 

You could also make a paper template to check your measurements.