I think that when we wrote the extension there wasn't an option to send through a subaccount.
I had a look at the docs and to send from a subaccount one need to provide the subaccount that should be used with the send function.
So currently you can't use subaccount with CMandrill. I'll try to add this in the next release.
I'm still in "evaluation" mode - as I have to work my way through a few clients and get their feedback on how they see their newsletter/emailing strategy is going to work in the future. At the moment, they're using RSJoomla!'s RSMail (which has a fair degree of reporting as well). CMandrill works well with RSMail, so at least we can do a decent comparative test!
No idea. Normally you should just select the subacocunt and we would sent through it. Are you sure that you've selected the subaccount. And do you perhaps have another site where you didn't select a subaccount so that mails get sent from the same api without the subaccount?