Its quite easy how it will work, Surely you have seen how a 2 station operation works on Big Thunder Mountain at all the disney Parks, there is a transfer track switching between the two stations before you enter one of the stations. When one train goes into one of the station, the transfer track will change for the next train to go into the other station and so on and so on. Also Batwing and X-Flight will be able to handle 3 Train operation increasing capasity even more where Stealth can only handle 2 Trains
Also, the reason they done it because there was complaints that unloading/loading was taking too long because of the complex restraints. Also with only 2 trains, it was slower even more. X-flight and Batwing will certaintly increase capasity by at least 50% I believe with these new changes.