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The tax ID is selected through a combination of Tax Zone (linked to supplier or customer) and Tax category (linked to inventory item) for example if I sell item A to Consumers (c) and also business (b) you will need the following;
item a linked to tax category containing tax id for 10% ex and 10%inc
consumer is linked to tax zone consumer containing tax id 10%inc
business is linked to tax zone business containing tax id 10% ex
When you transact against either consumer or business for item a it knows which one of the two tax id's to use linked to it through tax category, does this make sense?