Not sure exactly what you are asking here, but it is better to build near bonus resources, to use them (don't build directly on a 'bonus' or food resource, but building on a strategic, or luxury resource can be good).
Generally, you want cities on rivers, near bonus resources (for fast growth), and also be able to produce well (shields). You don't usually want to leave large areas that won't ever be used, but in the early game when food is so important, you may want to bypass some of the slow growing areas for awhile. You don't need to worry about every single tile, especially crap terrain like desert and tundra. Eventually, you want to use nearly every tile, and it is OK to miss 1 or 2 tiles here and there, but don't leave large tracts of land (10+ tiles) unused. Building cities *too* far apart will slow you down as it takes so much longer to get these cities up and running, distance corruption, and it is harder to defend these cities.