I never had any problem using equipment from different manufacturers. I use a simple beginners system (Uhlenbrock Daisy) which handle DCC and Maerklins Motorola II protocol at the same time without disturbing each other! Also I use decoders from ESU, MRC, Kuehn, UMELEC, QUANTUM-Sound, CT-electronics, Maerklin, ATLAS and TAMS and the same time. The only thing you've to attend is that more or less all system components have more or less features. That means for example that my central DCC system can handle only 5 functions but some decoders have up to 12 functions. Also my system can't perform a read-out of CV values from decoders. Maybe also some central DCC systems can't handle very old decoders with register programming but these decoders are non more in production. So finally I can tell you I never had any problem with compatibility!
One thing you've to keep in mind is if you want to control other equipment like turn-outs, signals, uncoupling devices,...
There are some different standards which have nothing to do with DCC. That means one manufacturer of DCC system use the "S88" bus, one other the "Loconet" or the xpressnet and so on.
Hartmut