Hi Noa,
Triggering a new profile shouldn't interfere with one that is already playing.
Try the following (viewing the output of ch1 and 2 on separate channels of an oscilloscope):
SF = 10000;
W.SamplingRate = SF;
Wave1 = ones(1,SF*4); % 4 seconds of 1V
Wave2 = ones(1,SF*4)*2; % 4 seconds of 2V
W.loadWaveform(1, Wave1);
W.loadWaveform(2, Wave2);
W.TriggerProfiles(1,:) = [1 0 0 0]; % Trigger profile 1 plays waveform 1 on ch1
W.TriggerProfiles(2,:) = [0 2 0 0]; % Trigger profile 2 plays waveform 2 on ch2
W.TriggerProfileEnable = 'On';
W.play(1); % Start waves + channels in trigger profile 1
pause(2);
W.play(2); % Start waves + channels in trigger profile 2
Please let me know if this is what you had in mind.
Thanks,
-Josh