Self-plagiarism in Publication-based commentary PhD thesis?
When compiling a dissertation, copying parts or entire sections from published papers is perfectly fine and standard behaviour. 

If a section is (mostly) identical with a published paper, it should say so clearly at the start. If the paper is submitted, but not yet published, you could either just treat it as published, and cite the submitted version; or you could use the text in the dissertation without further comment, and then add a note to the article that it is based on Section X of the dissertation.