Here is my method laid out into basic steps. Beersmith is a pretty important part:
1. Look at other peoples' recipes for beers that you feel are similar to the one you want to create. Look at ingredients, gravities, etc.
2. Figure out what malt flavors you'd like to have, and then what specialty grains you want to include. For instance, 1 lb crystal 60, 1/2 lb flaked wheat, 2oz black patent, etc.
3. Decide on a %ABV and body charactaristics, and add base malt or extract to reach an OG and decide on a mash profile that will result in the appropriate FG and %ABV. Now look at what percent each specialty grain is of the total fermentables and adjust if necessary.
4. Decide on how much bitterness you want, hop flavor, aroma, and what varieties. Add hops.
5. Choose a yeast to fit your desired flavor profile, temp requirements, attenuation and flocculation requirements.
6. Choose your desired carbonation level, the temp of the beer at bottling, and you'll have your priming sugar amount.
Obviously a book will take you way deeper. You can get down to water profile etc, but this is a start and it's my basic method.