For future reference, here are the momentum and braking settings I'm using on the locomotive fleet in order to use the ProtoThrottles:
Momentum (CV4) = 60, for Tsunami 1 and Tsunami 2, and CV4 = 215 for ESU (which LokProgrammer says is 53.75 seconds from full speed to stop)
Braking rate for Tsunami's is 41 + 128 = 169, which goes in CV 61 for Tsunami 1's and CV 117 and 118 for Tsunami 2's. For ESU's, CV 179 = 60 (which LokProgrammer says is a 15 second deceleration from full speed to stop).
(Also, I am using NCE advanced consists, programming the consists in the ops mode, which might be different from programming the consist address directly, but I'm not sure).
We had two successful op sessions recently with all three PT's working alongside NCE throttles and WiThrottles, with mixed consists of two or three diesels, and everyone seemed to like the braking, although some gave me feedback that the braking rate of 15 seconds wasn't quick enough. I had mapped all my locos to use F9 as the brake, so it was easily accessible to the regular NCE throttles as well as the PT's.