Single Board Computer vs System in Module

Hi guys,

I am facing a problem in my project, we have been using an Atmel microprocessor as the backbone, however we now face the problem of the USB connection; as I know it is highly not recommended to use these MCU as host to any USB device... so I just wonder, should I use the Single Board Computer or the system in module from the market instead of getting into serious problem??

Also what is the difference between the Single Board Computer and System in module?

Thanks