Well I'm getting there. Currently I've only programmed in Phase1 (what I've discussed here) with the latter Phases to be coming (however, the program does take the cycles from the Phase1 settings textbox). You can see how the tokens are transferred:

Also, you'll notice the light is on at the bottom. All this means (in this instance) is that one token is currently being held by the light - so that when you add up the tokens they should tally. 21 (counter) + 1x9 + 1x6 + 1x2 + 61x1 + 1 (light bulb) = 100. I should note the example portrayed in the screenshot is not an average count at the end of those 4 cycles, it's just a random case. The get averages button does nothing yet.