Season 3 still has the Table Rating system, I think, so you can scale the challenge level that way. 4-6 runners would be optimal (per design, IIRC), but I think it's workable with the two you have, since it looks like they're trying to fill the major roles. As long as they don't go looking for extra trouble, that is.
If you start running them through Season 4 or the CMPs (when they become available), they'll start needing extra help.