PhD Application, Mention of published Papers
I have seen different ways of this being handled but one way could be to write in brackets that you done around (50%) of the total work for the paper. 

It is more common than you think, many published PhD thesis have papers in which the PhD student is the final author in all of the papers inside the thesis, but they include a note that they where responsible for 50% of the work. 

Having papers published will look great regardless.