You've got your topic (or at least a general idea of something to explore), you've got an idea of where your primary sources might be — what now? This section will cover the basics of doing historical research and note taking.
Taking notes may seem like a straightforward thing to do, but there are a few pitfalls which can be easily avoided which will save you a lot of time in the end.
When taking notes, make sure to write as much information on the source's citation as you have available. You likely won't need all of this information for your final paper (formal citation will be covered later), but it will help you find the source again should you need to (as well as help anybody else who would like to find the source and contacts you). If you are dealing with boxed collections (usually full of individual folders), definitely make sure to note which boxes and which folders you looked at — even if you don't find anything useful in them. This will help you later if you suffer pangs of doubt about whether or not you missed something important.
There is no "right way" to take notes. The goal of notetaking is to have enough information as to use it later. Sometimes this will mean copying out long quotations, sometimes it will be brief summary notes. Most archives will make photocopies for you (for a price), which is another good reason to keeping careful track of citation information (should you later desire copies of something you looked at). When taking notes from books, keep careful track of which page numbers any information is coming from, as it will allow you to cite it thoroughly and convincingly.
After you've taken your notes, make a backup copy, whether they are on a computer or on actual paper. Never keep only one copy of your notes in any form, unless you enjoy re-doing a lot of tedious work. Never send your only copy of notes in any form of post or mail. Never leave them anywhere where water could even possibly do them damage. The historical discipline is full of stories of hard work gone to nought because of a tragic and unlikely accident.
Next section: Organizing your work