I'll give a how and a why. The how is that each club plays the other conference's teams once. So NYCFC would play at Seattle in Year 1 and then host Seattle in Year 2. For the East teams, NYCFC would at least host each once, and the 3rd game would alternate hosts every year. So year one, NYCFC would host Philadelphia 2 and play at Philly once, in year 2 NYCFC would travel twice host once.
The why is that MLS wants to reduce travel costs and therefore reduce the cross-country trips since most of the teams are on the coasts and therefore fills up matches with closer opponents to reduce the wear and tear.
As far as splitting the country up, that may be an option in the future. The only problem with that is that a lot of the stars of the league are in the West, people like Landon Donovan, Clint Dempsey, etc. If you completely divide the country, you can't do things like take them to New York and let them talk to the media (since a lot of the media is based in New York, specifically late night talk shows, morning shows, etc. as well as the TV execs who make decisions on how much to offer MLS for the TV rights.)