I have several MTH HO engines with proto 3.0. I run them as well as other HO engines that I have retrofitted with common DCC decoders (I use DigiTrax) and a DigiTrax DCS200 command station, PS2012, DT402, and PR3.
The PR3 connects the DigiTrax equipment to my PC (microsoft xp) where I run JMRI. I mostly use JMRI to control my HOs, MTH or otherwise.
There are some minor differences between regular DCC and MTH DCC. For example, on regular DCC you re-set the decoder by putting 8 into CV8. For the MTH decoder, you put 55 into CV55 to re-set it. There is also a special procedure to set the engine address to the cab number.
You just have to use the conventions for what the CV's mean that MTH defines.
For JMRI, there is no canned setup for an MTH decoder, so I just use the raw setup option when creating a new roster entry for an MTH engine.
CV3 and CV4 define acceleration for both regular DCC and MTH DCC.
Horn, Bell and Head-light functions are the same for both as far as JMRI is concerned on the JMRI throttle. Smoke on MTH is function 8. Cab and running light is function 5. Function 4 cycles the MTH station/freight sound effects. Just read the function and CV definitions at the back of the MTH manual that comes with each engine.
Not so difficult, what?
Oh, one more thing. The MTH decoder likes to have its sound effects turned on at the beginning of a session by cycling function 3. Cycle function 3 again at the end of the running session to shut the engine down. The engine will make nice startup and shutdown sound sequences as well as chuff and puff smoke in sync at a rate commensurate with the engine speed, and in sync with the drivers too!