Use RefWorks to store your annotation, and create a document with the proper format. To use it efficiently, you must do some manipulation. Use a format that includes Annotated with Abstracts - APA, MLA, or USGS have these formats.
When you download the record from a database it automatically loads the abstract of the article in the Abstracts field in RefWorks.
These formats will output whatever they find in the Abstracts field as the "annotation," so edit the Abstract field in the RefWorks record to replace the abstract with your own annotation.
Overview of the process
1. Collect citations in your personal RefWorks account as you discover them. Put the ones for the bibliography in one folder
2. As you read an article, take notes to capture your thoughts.
If the PDF is attached to your RefWorks record, read the article and take notes inside of RefWorks! Keeps everything together.
3. Edit the RefWorks record (click the pencil icon) to add your annotations in the Abstract field
4. Produce a formatted annotated bibliography using an Annotated with Abstracts "output style"
NOTE: Only a few output styles have a pre-packaged "Annotated with Abstracts" option:
But you can customize any output style to include annotations. See RefWorks help or ask for help from me.
Use the Annotated with Abstracts document output to create the format structure, then just replace the abstracts with your annotations.
The point of this is to use RefWorks for formatting. For example, APA style requires that your annoations be double-spaced; the format should be retained if you just replace the text of the abstracts in your document with your own annotations.
This method doesn't require you to put your annotations in RefWorks, but it does require that you keep them somewhere as you are reading the articles.