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Hello Gcj1971,
Welcome to the Community page,
So it does take the figure out of the CIS box but you just have to add it back in so if the labour amount is 1000 and you are on 20% CIS you would enter the 200/20% amount back in the box.
So for example on the invoice:
On line one you would do CIS Labour standard (20%) -amount 1000 -vat 20.0%RC CIS
On line two you would do CIS Labour gross (0%) -description materials- amount 200-vat 20.0% RC CIS
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