I employ my wife as company secretary, if I only work on 'relevant' engagements will I have to pay my wife out of taxed income?

You may only claim a deduction at Step 1 for the 5 per cent expense allowance and at Step 3 for any expenses incurred by the intermediary that would be allowable if you had incurred them and been employed by the client when working out the IR35 deemed payment. It is unlikely that any wage the company pays your wife for duties she performs for the company will be allowable at Step 3, however this will not affect the position regarding any deductions in the company accounts for her wages.