MIDI start/stop on command.

Do you mean you want to send a MIDI start signal at some arbitrary point in a project?
 
If that is the case I don't think you can unless it is recognised as a sysx message by the hardware. That will be in your hardware's documentation. You could then insert the message as either Sysx Data or as Sysx Bank (set up in Sonar's sysx view) using the event list view.
 
I've had a quick scan through all of my external hardware's MIDI implementation docs and despite there being loads of messages that can be sent "MIDI start" as a sysx message doesn't appear to be one of them.
 
Somebody may know better than me though in which case I'll happily be corrected.

You can not use Midi start/stop in that way. The way it is intended to work is as follows:

1) from a stopped condition, the master sends the slave the start position pointer which is a beat offset into the song.
2) master sends the continue command and the slave starts playback from the song position pointer.

A Midi Start message automatically causes all slaves to start from zero. The midi sync message has no position information and is used solely for synchronization. In effect, the start and continue messages do nothing on their own and must be followed by a midi clock message. The slaves count the midi clock messages to keep in sync. Slaves will not playback until the first midi sync message after a start or continue.

Sonar does not allow sending midi sync without also sending start, stop and continue.

What you are looking to do can be realized by using a combination of MTC and MMC. Sonar does support this. However very few hardware sequencers have that capability. In this case you would set up an external device with a chase delay, so that playback is delayed by a specific time relative to zero MTC time.
 
Does your hardware sequencer support triggering by midi CC or notes? For example, my Korg Karma WS supports RPPRs which are looped midi sequences triggered by a specific midi note (the midi sequences do not get transposed). The Karma is slaved to Sonar to receive midi sync. I then trigger the RPPR by sending a not on message at the appropriate time and playback is synchronized.

Hmm. Too bad you can't sync Dark Time to the Machinedrum via the DarkTime's Clk In and St/St In. 
Then you would be golden. :(
 
AAMF, You can try Turning the palyback on/off on the DarkTime's Clk In and St/St In. You'd need a midi clock to analog clock converter and a midi solutions relay which you can program to open/close the relay via a midi message. Just need to supply the correct voltage to the St/St In.
 
When all else fails, hack away. :D