Take notes when you read primary sources. Actively engage your primary sources by analyzing as you read, don't just passively read and summarize.
Record the citation information!
Apply keywords to your notes so you can sort them later (use cards or an electronic sorting system - it doesn't need to be complicated!)
Include your analysis in your notes
How does the information relate to your argument?
What questions does it answer or cause?
Draft a sentence on how this could be used in your paper
Think critically about primary sources by answering some or all of the following questions:
Who wrote the document (give as many details as you can, name, age, geographic location)?
Who is the subject?
What was the motivation for writing the document? Why was it written? (court transcripts, personal diary, committee minutes)
Does the form influence the content (would you expect to find the same kind of information in a diary entry as in transcripts for a court case?) How?
How did the account reach us?
How does it function in the broader context? What else do you know about this time period/person/region?
Make sure to indicate in your notes (maybe with a separate color) when you paraphrase and when you quote. You want to make sure that you do not inadvertently use a paraphrase or a quote without providing the proper citation. This would be plagiarizing.