You should first lay out the entire story you are creating on a storyboard. You are basically something similar to a comic book version of your animation--drawing out a picture-by-picture account of the show. This will serve as a guide for drawing the animation. If the show includes voice acting, you need to decide if you are going to draw and record the animation first and then record the voices to fit it or vice versa. American animators often employ the latter choice, while the former is common in Far Eastern anime.
The animation is drawn out on transparent plastic sheets called "cels." Each cel represents every slight movement that every character makes. You need to draw and paint thousands of these cels to make up the frames for the show, as a single second of recording takes 22 to 24 frames. Stack the cels for each character into piles in the order they will be used for easy access. The background/scenery cels will be painted separately and have the character cels placed on top of them during filming.
To record an animation scene, position your camera is over the painted scenery backdrop for the scene you are recording. The first frame of the scene is assembled by placing the character cels for that frame on top of the scenery drawing. This exact frame is recorded with just a split second of camera time, equal to the amount of time the shutter stays open when taking a photograph. The cels for the first frame are then removed and replaced with the cels for the next frame, which is recorded in the same way. This is repeated until the entire scene is recorded, frame by frame, shot by shot. Once every scene is recorded, then entire animated show can be uploaded to a movie editing computer program so it can be edited and mixed with the sound and voices, whether the audio was recorded before or after the video production.