Answer: The instruction from your vet might be indicate precisely when a particular medicine should be administered; for example, before or after meals. Many drugs which influence the digestion or absorption of food need to be given just before meals. Of the remaining drugs, most will be absorbed faster and more completely if they are not given at the same time as food.
When the instructions state that the medicine should be given certain number of times of a day, the intention is for the times of administration to be as equally spaced as possible. In other words, twice a day means every twelve hours, and three times a day every eight hours, insofar as this is feasible. Obviously it is not usually necessary to get up in the middle of the night to given medicine, and times of administration may have to be fitted around working hours, but as far as possible then even spacing of doses should be practiced.