Add it at bottling or kegging. The flavoring does not need to sit for a prolonged period if you do not add too much so adding it to the secondary would be redundant. The time in the bottles to carbonate should be plenty of time to get what you are looking for.
A tip for the amount to add:
Take a 1/2 pint and drop some of the flavoring in and taste, add a little more etc... until you are happy with the flavor then multiply out how many drops/weight to add for your batch volume.
Hope this helps,
Cheers.