LMSC I’m not 100% sure because in the end decided to close my limited company as trying to work within IR35 with a limited company too much hassle for the cost, However from what I read, it seemed like that intermediary paid the contracted rate to your limited company and you deduct 5% from it.
But then, you have to process the payments for both Employers and Employee NI, Apprenticeship levy and Employee tax. Pension etc You can no longer just pay the employee (ie you) the bare minimum either. In effect you become the employer.
For me, its not just worth the hassle. I am now retired as my work was in Nuclear Decommissioning and none of these contract were near my home so all costs of servicing the contract (travel, accommodation, food etc) had to be bourn from the Net rate after deductions