For the most part, it won't make difference in the flavor. Bittering is bittering, although some hops do give off a perceived harshness (Chinooks come to mind) that will affect the overall perception of the beer. For the most part, the flavor hops (30 min) and aroma hops (10-0 min) will just overpower any flavor you get from the battering hops.
In general, like the commercial brewers, just use high AA hops to get the best bang for you buck on hop purchases:)
Eat, drink, and be merry. For tomorrow we die. ~Dave Matthews~