When you start your new job your employer will give you a P46
On this form you have a multiple choice set of options - option A is as follows.
A – This is my first job since last 6 April and I have not been receiving taxable Jobseeker's Allowance, Employment and Support Allowance or taxable Incapacity Benefit or a state or occupational pension.
Providing the criteria mentioned are not applicable - I.e you can answer yes to this question, then tick box A and your employers should issue with a cumulative tax code rather than a w1/m1 code.This means on your first salary payment you will be allowed the YTD proportion of the personal allowance in full (approx £5600 minimum) before any tax is deducted.
and i suppose i have to keep paying class 2 NI and filling out self assessment every year whilst I am self employed
Providing your self employed earnings will be below approx £5k per year then you can apply for an exception from paying the class2 NI. Presuming you will be paying NI as an employee so it is probable that there will not be any added benefit in paying the self employed class2 if you do not need to - Employees who qualify for stamp get more generous benefits than the self employed.However the rules are quite technical and i would recommend doing some checks before you apply for the exception just in case this is not the case.
Link to CWF10 if you want to apply for exception
http://search2.hmrc.gov.uk/kb5/hmrc/forms/view.page?record=yKpjabZqCc8&formId=433
Details of what benefits you qualify for when you pay class2
http://www.hmrc.gov.uk/working/intro/class2.htm