Yeah, should be fine, the only issue you might have is if you have RAID setup as some ports may not be configured for it. Also different coloured ports may be on a different controller, some motherboards use the JMicron controller for 2 ports (with others on an Intel/nVidia one depending on the chipset), the devices will still works on a different controller but the features supported may differ (this won't be an issue for soemthing like an SATA optical drive).