If God had meant us to write out notes on cards, he would not have allowed us to invent standard notepaper or computer printers that take standard paper sizes. Be sure, however, to follow the right method. One of the important things you need to do is number the pages of your notes consecutively . If you have photocopies, put them in the right places in your notes and number them too. Keep your notes in a binder so pages don't get lost.
Some people prefer to print their notes onto paper.
In this case, the computer is just an input device, and notes are handled as above. If you are planning to use your notes in their electronic format, you need to determine how you want to set them up. Make sure you back up your information constantly if it's all in one file. You'd hate to lose the whole thing. As you gather sources, you need to keep track of them, including enough bibliographical information so that you won't have to go on a desperate search for a lost date or volume number when you start writing your paper.