The cables should run either on the front side of the bar or on the back side of the bar. NOT on the top of the bar where you rest your weight. Lots of bars even come with grooves front/back to house the cables under the tape.
The hoods can pretty much go where you want them. But they SHOULD be even! (choose the one you like, and tell the LBS to make the other match it?)
I'd take it back, and make the LBS do it over again right.
"If Americans want to live the American Dream, they should go to Denmark." - Richard Wilkinson