To get the Online Annual Questionnaire to auto populate information from your plan, you need to click the "Plan Question" button at the bottom of the Edit Online Annual Questionnaire form and insert those questions into your questionnaire. You can also access this option by selecting "Insert Plan Question" in the gear menu on any of the rows. Using this option, you can add checklist questions from the company or plan edit screens and it will use the current value of those questions as the default value in the Online Annual Questionnaire.
However, because the checklist questions are different for each checklist, you can't insert the plan checklist questions in the Default Online Annual Questionnaire, but you can still insert the company checklist questions using the "Plan Question" button. To use the plan checklist questions, you either need to go to each plan and set up the online annual questionnaire there or else use an Online Annual Questionnaire batch and set the checklist for the batch by clicking the "Change Filter" button when editing the batch. Once the checklist has been set in the batch, you can add the plan checklist questions while editing the batch questionnaire.