Welding can be done two ways, butt welding or lap welding. Butt welding may be a bit harder than lap welding for most people but will have the preferred finish. While welding an over-lapped flange is easier to do it will leave a seam that could trap moisture unless properly sealed after welding and then of course it will be obvious if it is in an area that is seen with the trunk open. Personally I prefer butt welding and on metal this thin that is usually accomplished by using a series of tacks until the entire seam is finished, can be time consuming but you will be rewarded with a very professional looking repair.
Don't disregard the suggestion to bond that skin on, this is something I intend to do if I do another one for myself. So far I have not been able to convince the owners on any I have done that this is an acceptable way of doing things but it IS!