Different artists have different ideas on how to design your Anime. Some prefer to write the entire script out before working on their images. Some prefer to go panel by panel, writing one panel and then drawing it before working on writing the next one. It is generally a good idea to start with at least a basic outline. This will help you ensure that you are pacing well and that you do not leave out key elements you will later have to go back and add in.
There are several ideas for inspiration for people who are unsure of how to start designing their own Anime. One idea is to study art history. Understanding the dynamics of art before you get started can be a great tool. Do not just read up on or look at pieces of art that will apply specifically to your work. Understanding the history of your art and what came before it can give you a better understanding of the art you are working on. It can also give you ideas on how to incorporate different elements into your Anime that you had not considered.
Reading different drawing technique books can be a huge help as well. No matter how good an artist is, there's always room for improvement. Taking advantage of different drawing exercises can be immensely rewarding in a number of ways. They will rarely force you to think outside the box by doing exercises on things you are not used to doing. Stretching your imagination will help you to be more creative in your own work. It'll also help you to learn what your strengths and weaknesses are. Some artists would never know that they were particularly talented in drawing certain action scenes or particular body shapes if they did not force themselves to try drawing exercises.
Of course drawing your Anime is only half of your design. You also want to make sure you have effective and interesting writing as well. No matter how good your drawings are or how well you shade your panels, if the story is uninteresting or written poorly your reader will not be interested. Study up on writing books to learn proper techniques for creating tension, pacing and other aspects of writing. You can also go back and study examples that you particularly like. Reading you favorite Anime with a more critical eye can be very helpful. Pay attention to the way the writer worked on their dialog, transitions and other aspects of their writing. Make a note of the things that did and did not work for you and plan your own art accordingly.