Recipe design is a never ending process. You also need to think of the recipe as a whole (grains, hops, yeast, flavoring components) to try to maintain a balance. Each part should support and compliment the others.
Much of the hop choices depend upon whether or not I am trying to brew to a certain style. If I am, I will be selecting grains and hops to fit that style of beer. The style guidelines give you aroma, flavor, color, bitterness, and body targets, so everything must balance out to match the pre-determined expectation.
When brewing off-style, I am usually thinking about a given flavor impression that I want to highlight. Usually it is based upon a given hop aroma/flavor and this becomes the focal point for selection of the other hops, grains, yeast, etc. for the recipe. mrgrimm101 has it right when he says to select other hops that support the base flavors and possibly expand the palette a little bit and add a little more complexity.
The same goes for the malt selections. If I want the hops to dominate the flavors, such as in most IPAs, I will lean heavily on the base malt and go light on the character malts so they don't detract from the hops aromas and flavors. If I am looking to brew something more malt dominated, I choose more subtle hops if I want any hop presence or more neutral bittering hops if I want just the malts to be apparent and balance out any residual sweetness.
Then you can look at yeasts which accentuate malt flavors, finish really dry, and/or give characteristic flavors themselves.
When I design a recipe, I am usually thinking that it will take 3 to 5 repeats to get the recipe to be in balance and have the exact flavors I envision from the beginning. Taking careful notes on the aromas and flavors you create or discover along the way helps greatly. Overall, I feel that I've been lucky in that most of my later recipes seem to fit in quickly to the profile I wanted from the start and only minor tweaks are needed from that point.
A good source for hops aromas that will help you determine which play well together is the aroma wheel at
www.hopunion.com. For malts, I am a firm believer in chewing on some to get the basic flavors of each malt down in your memory and then chewing on a mixed handful to give yourself some idea of how they behave when mixed.