Typically, the cylinders of a car’s engine are lined up along the crank (making it “inline” or “straight”), or divided into two banks and angled away from one another (the result being the “V” formation).
Between the inline layout and the vee layout, one key difference is the shape of the resulting engine. Say you have six cylinders of identical displacement/size. The inline-6 arrangement (such as the one in the BMW M3) will be long and narrow, while the vee-6 arrangement (such as the one in the Audi A6 3.0) will be shorter and wider.
Most of the time, carmakers opt for the V6 configuration instead of the inline-6 configuration because of packaging reasons. It’s just easier to park a short and wide motor/block under the bonnet than a relatively skinny and lengthy one.