A client of mine has some emplyment income through I-PAYE from Just Payroll & Umbrella Company(which has been taxed at source) from a Contractor even though he is Self- employed. Do I put these into the books and if so how, or do I leave them out compleatly?
This sounds like one of those tax avoidance companies. Firstly, you need to check wether your client has been set up as a Ltd Co. by this company, that is the normal practice. If so, then any income paid is via the Ltd Co and the tax will still need claiming back. A complicated one, best left to the accountant. You will still need to enter the income (gross) and show the deductions. These deductions will be used when compiling the S/A return at the end of the tax year.
I would suggest liasing with your clients accountant to see exactly how they want you to handle this.