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I have a number of plain text files that I created in Notepad (or Wordpad) and transferred to the Kindle using the USB cable. With the "notes" feature of the Kindle, you can use its keyboard to type in notes that will be associated with your text file. Transfer the original text file and the MyClippings.txt file to your PC, then copy/paste your notes from the MyClippings file either into the original text file or into a new file, depending on what you want to do next. For example, I can have the equivalent of a Tweet file right on my Kindle by starting with a small text file named diary.txt. I then create notes for this file which can be read at any time on the Kindle and which are stored in the MyClippings.txt file. Periodically, I transfer the MyClippings.txt file back to the PC, copy/paste the notes back into the diary.txt file and then transfer the new diary.txt file back to the Kindle. I just delete the MyClippings.txt file from the Kindle and it will create a brand-new one the next time I go to create a note.
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