"When teaching the IMC course do you log it towards IFR flight time?"
In accordance with Art 35 you log what you are doing however there is no requirement to log IFR, only Instrument Flight time which is described in JAR-FCL1.001.
Its your personal log and you can enter whatever you want however; whether anyone else accepts it for anything is another matter. You require a certain amount for an ATPL issue thereafter, Instrument time in the log is of little use for anything. If you were an airline pilot hoping to be an IRI only that flight time that was clearly IFR would be accepted toward the 800 hours requirred. In the case of a FI you only need 50 hours Flight by Sole Reference to Instruments to teach for an IR. By the time you have met all the other requirements to teach for an IR you could not possibly have insufficient hours.
So if you want to log IFR, assuming you were operating IFR then there is nothing to stop you but it really isn't a lot of use and most log books don't even have a column for it.