I have three carousels running at the same time, each with their own unique ID. They're being called using an attribute selector like so:
So each carousel has an id that begins exactly with the ID of #myCarousel and then a number to set them apart.
But you can also define an instance for each carousel on the same line, for example: (Notice how each selector is separated by a comma.)
$('#myCarousel1, #myCarousel2, #differentCarousel3').carousel();
And it will work as well, so just make sure you use a valid selector for each instance of your carousels.