Hello!
OD cost matrix is used to find the distances between sets of locations. You can constrain the search based on a distance cutoff as well as a # of locations to reach from each origin.
In your case, you are more interested in the distance between each CBOC and its parent VAMC. I think the more appropriate solver solution would be batch routing. Within a single Route analysis layer (or multiple, if you run into memory issues), load every CBOC, being sure to give the location a RouteName value that uniquely identifies that route. Perhaps you could use the CBOC id as the route name.
Next, for every CBOC, load its parent VMAC, giving it the same RouteName you gave the CBOC. This will result in certain VMACs being loaded multiple times, which is fine, because they will have different RouteNames. Now, when you solve the analysis, you will get one route for each CBOC/VMAC pair.