QB Issue Resolution:
The vat codes control this from the underlying vat items.
The vat code is a holder for the vat items or groups and the items control where the vat is posted and the nett amount so a single vat code can have a vat item fro sales and a vat item for purchases.
But if you need ,more complicated set up then you use a vat group that can have more than two vat items attached to it.
It sounds as if your vat set up is not correct or the items attached to the vat code you used.
Resolution for Issue '“How do I connect a bill to a input VAT account?' available: Yes (Solved).
Source: Intuit Community forum.
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