You can add annotations to your citations using NoodleTools at any time. Start by adding a "new source".
If you import the citation directly from a database using the NoodleTools button, you will need to "tweak the citation manually" and then scroll down until you see the box for typing in your annotation.
After you click "Save" and return to your list of citations, you will see the annotation directly below your citation.
If you "copy and paste" a citation into NoodleTools, you can also add an annotation. Immediately after copying and pasting the citation, scroll down a little further until you see an annotation box. Write your annotation and click "save".
If you already have a citation and need to go back and add annotations, just click on the 3 dots to the right and select "edit". Scroll down until you see the annotation box. Type up your annotation and click "Save".
Two citations with annotations added are shown below.