If the aircraft is approved for multi-crew operations, trough it's AOC/local CAA you will accrue multi crew hours on the type.
I know this, as I had a chance of getting on a King-air some time ago, the condition that the AOC had to state that it was multi-crew operations, I would assume there would be something similar in other countries too, if not you would not be able to log the hours at all when flying on single-crew aircraft.
From what I understood to get the JAR ATPL issued you will have to take that on a proper multi-crew aircraft though, not on example the King-air, that was one of the reasons I was reluctant, as in theory would have meant I would have had to pay for 2 TR's.
I am not expert on this area, but this is based on the experience and the research I did around this area around 12 months ago. The ATPL must be on a JAR CS 25 aircraft, while I think you probably flying on a JAR CS 23, aircraft that is single crew ops, but probably I assume your company has a special approval to use it as multi-crew from their local CAA.
One thing I was warned about when considering this, was to check with the operator that they actually was properly approved to use multi-crew flying on a normal single crew airplane, as unless approved it would not be possible to log it. And there was stories of operators that did some not tell the whole truth about this to their pilots.