There is actually a feature for explicitly stating which graphs to search:
The graphMask variable on the NNConstraint is not much used (or mentioned), but in the cases where it is useful, it is really useful.
The graphMask enables you to set, for each path, what graphs it should be able to search (or actually, find start and endpoints on).
ABPath p = ABPath.Construct (transform.position, blah, null); p.nnConstraint.graphMask = 1 << 0; seeker.StartPath(p);
The above code will ensure that only the first graph is searched for close points (read up on bitmasks if you have no idea what “1 << 0” does).
However, there is another, much easier way to do what you want.
You can enable A* Inspector -> Settings -> Pathfinding -> Full Get Nearest Node Search.
That will make the get nearest node code search for the closest ‘valid’ node on all graphs instead of first choosing the graph by checking the closest node (even if it is not valid). It is disabled per default because it is slower having it enabled, and it is rarely needed (most people only use one graph anyway).
See http://arongranberg.com/astar/docs/class_astar_path.php#a10d5c41cd51043fb472da8692ffb1577
PS: If you do not want the last vertex in the path to be the exact requested point, adjust the Seeker -> StartEndModifier settings, for example setting End Point to ClosestOnNode.