Brainstorm and storyboard (create "mockups" of the visual treatment) the opening logo sequence in detail. Identify what visual elements are needed (text only, a company logo, an animated sequence) and how they will interact on the screen. Plan the timing of the sequence. Does a logo fly in from the background and then text appears underneath? Will some elements repeat, such as a spotlight effect sweeping over the background?
Assemble all the required elements, making sure the resolution (number of pixels per inch) matches the format you will be finishing in. A small bitmap (made of individual pixels) graphic will show jagged edges if scaled too large. Similarly, a high resolution scan may be larger than necessary and slow down your computer if you don't require so a lot of detail in the format you are delivering.
Name your files carefully to not lose track of elements later on. Maintain consistency in naming and organizing materials in case you need to deconstruct a complicated animation or replace one element among many later on.
Create a new After Effects project and import and organize all your footage. After Effects allows you to create folders to group materials however you wish. One folder could hold video footage, another stills or scanned photographs, and another graphic elements or animations. Keep note of where you place elements within the folders of your project. For complicated projects, keeping explicit notes on how your materials are organized, what kinds of materials you are working with, and how you are using different elements, provides a useful repository for easy-to-forget details about your project. Keeping track of versions of materials and edited sequences also provides an external reference to avoid confusion later on. Often when a sequence is being edited, output for approvals, and then modified again, it is easy to end up working on the wrong version and having to redo your work.
Build a composition (what After Effects calls an edited sequence of material) and start executing the design of your opening logo. After Effects allows elements to be moved over time, resized, duplicated, colorized, placed in three dimensions, among hundreds of other effects. You can animate the movement of the "camera" (essentially the point of view of the final audience) to move around a composition adding action to stills, texts or other static elements. After Effects contains many of the same image manipulations
Output the finished animation to be integrated in your film project. Ensure that the size, video compression and audio settings match the format of your film.