Firstly, good luck getting agent who knows the rules (probably won't work in your favour). If you do get an agent who knows how to use the manual system, which many of them are no longer allowed to, the system won't price the itinerary if it has any "peculiarities" (mixed classes, stopovers, open jaws) and you can't pay for it. Most agents just punch in the O&D using the same online system. I'm not sure if stopovers are officially allowed or not, but I doubt anyone in LM has the definitive answer either, judging by how well run the program is

I'd be glad to be proven wrong, though!