NoodleTools has features that respond directly to multiple aspects of this assignment. You are being asked to focus your topic, create an annotated bibliography and to use your sources as evidence in your paper.
NoodleTools allows you to:
Save source citations and create annotations within the tool.
Record thoughts, questions and keywords you want to explore in notecards
Create notecards where you can pull quotations and create paraphrases and other notes to make it easy to find your sources and to remember why you wanted to use them in the first place.
Create outlines and drag and drop sources into it
Create and export formatted references
Throughout this process, I'll mention places where I think you can use the tool.