I've not had a chance to do a brick array before, but since I use a 15-in Gerber plotter, I have had to tile many of our larger projects and the process is identical.
Some design programs are capable of automatically tiling your artwork. You just specify the tile sizes and the program does the rest...or so they say. I've never been fortunate enough to have simple enough layouts to do it that way though. My large stencil layouts resemble more of a jig saw puzzle instead of a Sudoku board. Most automatically tiled layouts involve a certain degree of overlap between sections, but you shouldn't specify any overlap in your case.
(I question the feasibility of auto tiling since you will need to accurately cut full boundaries for each tile. In the case of vinyl signage, the accuracy between tiles is not so much of an issue because the vinyl is applied to a single substrate...not 100 individual pieces)
Stencil is expensive, and I personally take the manual approach so I know exactly what to expect. It involves applying grid lines (the size of your pavers) to the layout and then trimming out individual copies of each section. I use AutoCAD for this process because it's extremely accurate and relatively fast. It can be tedious, but the best part is that I never have any surprises whatsoever. The last thing you need is 100 pieces of stencil that don't match up. In real-world terms, that would boil down to approx. $500 of scrap, plus labor.
If you've been at this for only 6 months, it's going to be a daunting task if you don't have any prior design experience. Send me a PM if you need clarification.
As far as engraving goes, you're going to want to blast them as an array since they will have incised surfaces across joint lines. This involves applying a 1" or 2" wide strip of stencil between adjacent pavers (on the sides of the pavers). Make sure the edge of the stencil remains perfectly flush with the top of the pavers. This stencil will prevent the abrasive from eroding between the joints.
Next, lay the pavers on the floor in your blast room and bind them together using ratchet binder straps. Apply the cut stencils to each section and then mask off the joints with narrow strips of stencil as needed. Then blast away. Some companies are capable of doing do this in a vertical manner with some sort of fixture.
I'm sure there are other ways of doing it, but that's just my $.02.
JB