Check the criteria of ee and figure out which category you are under and provide the related documents for application.
Currently you can apply though Federal Skilled Worker/trader (requiring foreign work experience), Canadian Experience Class (requiring at least 1 yr of Canadian working experience) and Provincial Nominee Program. Each program has its own criteria. EE is only a ranking system to quantify how likely you can be accepted for immigration and issue invitation to apply after a candidate is deemed qualified.
Previously Canada issued PR to phd students as a means to attract students. The policy was cancel by conservatives couple of years ago. I dont think you will be approved for PR only because you are in a phd program. But maybe you have work experience so please study the programs aforementioned to decide which one fits you well and apply.
Each province has its own policies for PNP. Maybe there is a province allow current phd students to be sponsored by its PNP. Again you gotta figure it out.