We need to know your computer brand, model, and configuration.
You cannot set aside a USB port for one use, unless you have only that USB port connected at start-up, then connect the other devices which will be using USB ports afterward.
The Scanner will not care which USB port it gets, but on some computers, the USB access is weaked by having too many things connected.
If this is a laptop, or if you have a number of things which need to be connected to USB, I would buy a powered USB reader of quality, such as Adaptec, or if a desktop, add a quality USB card in one of the PCI slots.
Cost for either should be about $25 to $35 depending on where you get it. The Adaptec will be a lot more, but will work a lot better.