It is easier to create notecards after you have added books for the project into a bibliography. Click on New Notecard to create a note card. Using the Source drop-down box, select from your bibliography the source that this notecard references. Fill in other information and save.
Once you save it, the new card drops into a holding area on the left side of the screen. Drag it onto your tabletop (center of screen) for editing later. Cards can be moved freely on the tabletop. This working area expands according to your needs; only a small portion is visible at any one time. A rectangular area at the bottom left corner allows you to navigate around your tabletop.
Double clicking a card allows you to edit it; CRTL-CLICK a card to select (or de-select). Do this to add a card into a pile, or retroactively assign a source from your bibliography to the card.
Outline
The right-hand panel helps you create an outline for your paper. Click the green + sign to add a chapter or subchapter into the outline. The Move Left and Move Right buttons allow you to promote a subchapter into a chapter and vice versa.
If the Citation with NoodleTools guide does not answer your question, take a look at the links below.