In my BIOS there is a boot order where you can set which drive is first and so on, I would guess your machine is similar. I'm assuming setting the boot order would determine which drive boots first, you will probably have to enter the BIOS and change your new cloned drive to be first in the order.
I myself Cloned my SATA boot drive to another when I first got my computer, but I switched the data cable for the boot drive to the cloned drive and don't use the original. I only use the Original drive if I get into trouble with the cloned one.
It may be a waste of a drive but it's set as the machine was new, I guess you could call it a factory restore partition only on a full drive lol.