Right then.
You need to set in the ignition settings menu the 'Ignition outputs in use in h[2]' to '2..0', 'Ignition driver type' to 'Dummy'
In ignition outputs menue, set 'Ignition outputs in use in h[2] table' to '2..0' unless you are using some of the Ignition outputs for other things such as relays or shift lights, in which case it will be different. Then select which output to use on the table entries (listed in a column down the left) using the drop down boxes on the right, selecting the IGBToutputs highlighted with the EC36 pin numbers that you have wired the coils to.
Basicaly your h[2] table should look something like this h[2]=20 10 30 00 00 00 00 00 depending on the firing order.
Not being overly familiar with rotary engines, i cant help with the firing order or final set up, but i hope i have given you an idea what to be looking for.
Wait for Rob to confirm this before you try it on the engine, like i said, i havent any experience on a rotary engine