Many PhD students are challenged by a familiar set of problems and issues, which are familiar to experienced supervisors and have been written about extensively. If you are thinking about doing a PhD, or you are engaged in one, I strongly recommend these books:
White, B (2011) Mapping your thesis: the comprehensive manual of theory and techniques for masters and doctoral research. Camberwell, Victoria: Australian Council Educational Research. ISBN 978-0-86431-823-7
Phillips, E.M. and D.S. Pugh (2010) How to get a PhD. 5th ed. Milton Keynes: Open University Press. ISBN 978-0335242023
Petre, M and Rugg, G (2010) The unwritten rules of PhD research (2nd ed). Milton Keynes: Open University Press. ISBN 0-335-21344-8
Creswell, R (2013) Research design: Qualitative, Quantitative, and Mixed Methods Approaches. 4ed. London: Sage. ISBN 9781452274614.