The design and conguration - where to put the wings for example - are part of the design process and the positioning (eng/wing) is derived at by a design and config process that establishes the final A/C function
starting from a blank piece of paper, the top level requirements are established, basically, from here you figure out what it's suppossed to do - move people or freight ect, what engines are avialble, what the MTOW, MRW , what the mission requirements are (how far, high, fast does it have to go) and so on. military customers have different requirements from civil customers with corresponding different levels of structural and systems redundancy with equally frustrating weight penalties
in the early design phase weight is key driver, eg, if you have a high wing definition, putting the LGD on the wing requires the beefing up of the wing primary structure up to cope with the wing (limit/ultim') loads ect, but the ground handling is better (eg f-27).then what do the weight penalties do to the performance - fuel burn, A/C dynamic stability (particualrly at low speed): from this point on there's a massive bun fight between all contributing depts - engineering/aero dynamics ect until a compromise is arrivied at.
the easiest way to figure out why any specific config has been adpoted is to ask 'what is the plane suppossed to be doing and how do you get things (people or freight) in and out of it', from then on it's relatively simple.