iPhoto to iCloud - I'm so confused

Ok, so my wife upgraded from 4S to 6S today. As it's supposed to, any photo we take with the 6S uploads automatically to iCloud. We thought now would be a good time to backup the photos from the 4S to the cloud (we haven't done it in a while). There seems to not be an easy way to do this except to upload it into iPhoto and then upload those to the Cloud. Or is there?

Anyway, while doing that, I thought that I should upload all old photos in iPhoto (all 11,000 of them) to the Cloud while I was at it. It was working swimmingly....until we realized as I was uploading the photos to iCloud they were appearing in my wife's new phone. And, if we deleted one of the newly uploaded photos from her phone - it deleted it from iCloud.

Clear. As. Mud.

Anyway, is there a way to backup all iPhoto pics to the Cloud without them showing up on my wife's phone?

I haz teh dumb.

Thanks in advance!