OK, The PRIMARY coil is the one in the side, thru the rocker cover. The SECONDARY is underneath. The SECONDARY is there to clean up the emissions so is not the MAIN spark.
If the PRIMARY coil fails, the fuel being injected would just go through and come out the exhaust as neat(ish) fuel, also known as HYDROCARBONS, not good.......So, in the event of PRIMARY coil failure, the SECONDARY tries to burn off the HYDROCARBONS by firing off. (are you with me so far!)
To test is easy peasy. Run bike on centre stand, (not too long mind

),use a pair of INSULATED plug pliers, (you'll understand why if you don't

), and pull off the SECONDARY plug cap. Now of the PRIMARY is not working, the bike will REALLY mis-fire!!!
There is a slightly easier way to test the PRIMARY but it's very dependant on whether the bike is 'set up' right.
Try again on the other side, PM me if you don't get it!!!
Good luck!!!
Smudger