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Hi, Sam here , one of the UK tax Experts here on Just Answer, thank you for your question and I shall reply shortly
Thanks for your patience
ALL your income from this employer should be salary under PAYE as this is not true self employed income so should not be put through the limited company but ALL paid through the employee/employer salary arrangement so your employer and you are both in breach of possible IR35 but very much of employment status legislation so this should be rectified as a matter of urgency and I am surprised the employer condones this or that your accountant has not raised this as an issue before now.
Let me know if I can assist further