One of the specs is the number of designs on your board. Some companies will charge extra for multiple designs, even if you're not asking them to cut V-grooves or otherwise separate them

Assuming you are referring to the smart prototyping PCB service, you must use V-grooves rather than drilled holes.

What I usually do is panelize my design, using something like CAM350. I clear out 1/4" or more between any copper feature for each instantiation of the board. Then I just submit it like that, when it comes back I just cut them out on my band saw.