Hello, I have to say: "yes, you can set the bookmark onto the right side of flash window with using Boxoft PDF to Flipbook software".
Here are steps in detail.Step1: Running Boxoft PDF to Flipbook on your computer and then import PDF file for conversion;
Step2: Select Classical template among from flash templates box;
Step3: Find out bookmark bar on Design Setting panel, then choice Right option in Panel Position;
Step4: apply changes, you will see the bookmark has remove to right side of flash window.