The little black flies on the shoulders or sides are horn flies, they suck a lot of blood and are considered the most costly fly by the USDA - every pound of blood they suck has to be replaced by feed they eat and affects milk production and/or body condition.  The most effective way to control horn flies is by feeding Methoprene (also known as IGR or Altosid) though the mineral or feed.  Cost per ton of mineral will look shocking, but at a 4 oz feeding rate the actual cost should be about 90 cents per cow per month.  For other flies (face flies, horse flies, stable flies, etc) methoprene will help some but we've found a combination of ear tags (rotate the active ingredient in the ear tag every year) and dust bag/oiler/spray work the best.