The Veritas "Bookshelf" speakers you have are almost misnamed. They are more like "midget towers" - My apologies to any little people reading this...
Any drawbacks commonly associated with bookshelf speakers doesn't really apply - except one: the small cabinet requires the midbass speaker to WORK for low frequency output (compared to a larger enclosure) and that makes the speakers power-hungry. You are giving up efficiency and getting a smaller cabinet size.
The fact that it is a three-way design helps because you are asking very little of the midbass 6.5" driver. If it were a two-way design, the better bet would clearly be running them as "small" but in this case, it all depends on how the lower frequencies interact with your room (and amplifier). Be aware, too, that running them as "large" uses considerably more power! Try both and go with what sounds best.
P.S. - Good find on the speakers! $700 is a smoking deal!