I would stay away from C#, since you are working PHP currently I'd stick with it. The barcode reader will probably be implemented with javascript or java anyway and you can use it to populate a hidden form element and then go from there.
I'd look into the documentation that comes with your barcode reader and make sure there is a web site integration example and it should answer your questions. If you want our help, as long as you have that documentation, we could help you integrate it in a premier support ticket.