Honestly, I do my own manga for fun, and I don't use a fancy program like Manga Studio to help me lay out storyboards and script. All I need is a digital painter program (Photoshop at the moment), to help with text, shading, etc. I had the same problem you had just recently too. I can't tell you what you need to do, every artist has their own way of doing things. I hope you have a script ready. It's too difficult to draw storyboards without a good script. If you're really serious about the story, you can have someone else review the script to finalize story, character, flow, dialogue, etc. Thumbnail sketches (story boarding) can pretty much be drawn anywhere, though sketchbook would be best, because it's just a way for you to plan the actual page. It's good to know where you want your text placed and stuff.
Although having Manga Studio and other software programs make the process easy, the hardest part is actually developing the story and characters and keeping it interesting and intriguing.
