Do not commence work without thus Software. End-notes is a popular state of the art for most fields. Start entering your bibliographic citations, choice quotes or insights, and categorizing them by topic and subtopic as you read. Never read a source and postpone entry, relying on handwritten notes alone. Handwritten notes rarely facilitate access to information unless you know where you are going from the outset and have a hypercard mind.
Data resist reorganization to accommodate inevitable changes down the line.
Read a little, write a little must be your mantra. Entering notes is not enough. You must put yourself and your thesis in the driver's seat. Information alone doth not a dissertation make. No fewer than one monthly.