Yes, the key to stock tracking is to choose the right unit of measurment. It is this that you need to be able to specifiy both your sales and purchases in.
For bottled beers and ciders the measurement unit would be "bottle". Your "Order Unit" could then be set to bottle as well, in which case "Order Size" will be set to 1, or you could choose to set it to "case" in which case "Order Size" will be set to the number of bottles in a case.
Be aware that if your order unit is set to case, you will have to provide your stock count in terms of cases also. For example, 0.5 cases, instead of 6 bottles.