Hi @DaveDos 

I think you're mistaking what QBO is for.  It's accounting - to give your profit/loss, etc - it isn't tax filing software.

At the end of the financial year, QBO will give you (assuming everything has been entered correctly) your gross profit for the year - if you're self-employed, that's your top-line earnings if you like.

When you come to complete your tax return, that's when the allowances come into play - the allowances are entered into the return, not into QBO.

(in effect the allowances increase your tax code rather than decrease your earnings)

Hope that helps.