It is a common problem, that whilst the two locos may come from the same manufacturer, with even the same decoder, unless they are the same exact model there can be slight differences between them when consisted together.
The best thing to do if at all possible is to try and set up a small circle or a round-and-round circuit where you can let the two locos chase their tails so to speak. This way you can observe which one appears to run faster etc and compare the running characteristics. You can then adjust the appropriate CVs until both run similarly without catching each other up. If you can use POM programming, (Program On Main) then you can adjust these values with the locos still on the track so no need to move them to a separate programming track. Another thought might be to use something like JMRI, the QSI computer programmer and something similar so that you can setup all the speed profiles on the computer, which is easier to visualise than tweaking the speed step CVs one by one.
As for the right settings I think it might be a case of trial and error here. This is a common process though in the smaller scales like HO and N where they are regularly consisting 3-5 locos together. I would have a look at the material aimed towards this as it will all apply to large scale too. Even some of the books from the Model Railroader magazine guys under Kalmbach Publishing are really good and very straight forward guides in plain english. Some US DCC forums might be good too, is there an NCE users forum? Someone might have some good tips for your specific system?
Sorry I can't be more help for an NCE setup, but these are just some general tips and ideas I've read and picked up along the way.
Best wishes,
G
