Is there a fix for a flat garage roof that puddles in the middle other than paying to have the entire roof done over ?

If you can access the roof joists, jack up in the low spot and sister new joists to the old. Span af least 3-4 ft part the low spot. Make the new joist as large as or 1 size larger. Puddling like you indicate is caused by bowed joists, usually too small. Lag or carriage bolt the new joists, don't nail. If it is a 2 car garage, and you have space, consider a middle wall or support columns. The roof should never be flat, but should have at least a 1/12 pitch and be a hot.mopped or membrane roof.