What I see most restorers do is drill strait though the old spot welds for the trunk and front toe board panels. Then they would fill the old hole with weld to attach the new metal. With enough practice you can make it look like a factory spot weld. However you will need to drill holes to on the floor boards to attach it to rocker.

I'm all for the factory appearence look but in the end how many people are actully looking under your car. Seam weld will do just fine as well.