Create an outline for your instruction manual listing all tasks and subtasks in the order you decide upon. Microsoft Word contains an outlining feature that will automate the process for you.
Include space in your format for all the various parts of instruction manuals, including such sections as table of contents, an index, diagrams of parts showing how to assemble them, usage instructions and any other sections relevant to your technical content. Not all sections will be required for all manuals, so depending on what your instruction manual is for, add or subtract these from the outline. Make the outline as detailed as possible so that the manual will be easier to write in final form.
Decide what the manual format will be. If it is a collection of self-contained tasks, like a cookbook, you have more presentation options than if the manual is a set of sequential subtasks that lead to an overall result, such as a manual showing you how to disassemble an engine.
If you need to replicate the information in several formats (such as printed pages, computer screens, and cell phone screens) you may want to use a "single sourcing" framework like XML and DITA. These tools let you separate the information from the format so the information can be "repurposed" more easily. If you decide to "single source" your information, plan for it as early in the process as possible. You will produce blocks of information ("topics") and multiple delivery formats, requiring multiple graphic layouts.
Create a layout in a page design program such as FrameMaker (for text-heavy projects whose format does not change much from page to page) or InDesign (for graphics-heavy projects, or manuals where the basic visual design varies from page to page).