I have been both employed and self employed on and off for over 10 years and have ten years worth of self assessment tax returns.
Your employed income is taxed through PAYE on your payslip. This will not change whether you are self employed as well or not.
You will need to declare your employed income on your tax return, but as long as you have been paying the correct tax, this will not affect the amount you have to pay.
The first £1000 you earn self-employed is not taxed (but you still have to declare it). This is sort of like a specifically self-employed personal allowance.
I have an accountant now, she charges me around £250 to do my tax return and answer my many queries.