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Hi Adrian
Like Marilyn says - any income you've earned since April, as an employee, will be shown on a P60 at the end of the tax year (or a P45 if you leave before the end of the tax year) so you should keep these payslips totally seperate from your self employed payment certificates. If you get them mixed up, and then report employed income on your self employed pages of the tax return, you could end up paying tax on that income again! This income and total tax deducted will be reported on the Employed (pink) pages of your self assessment.
When you work as a CIS sub-contractor, you will be invoicing your contractor - then when he pays your bills, he should be giving you a certificate/payslip to show how much CIS tax he has withheld from your invoice. You will need to keep all these certificates together as your proof, total them together, and 'claim' this 'CIS Suffered' on your tax return as tax already paid.
On your tax return for self employment (orange pages), you will need to report all of your income (the amount you billed your contractors for all work) and all of your expenses - i.e. materials bought, fuel costs or mileage allowances, telephone costs etc and you will pay tax on your net profit - but the amount of CIS Suffered above will be deducted from this total amount.
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