Your healthy extra choices are seperate to your syn count.
For example, if you have 35g porridge with 250ml semi-skimmed milk in the morning, those are both your A & B choices.
If you then later in the day have cheese, or ryvita, or something else from the healthy extra lists, you will need to count them within your syns.
Does that make it any clearer??
It can be confusing, especially at first, but you will get used to it