Generally, the tax people want to know about new business start ups so that they can ensure that self employed business owners make interim payments of tax as appropriate due during the course of a tax year. Notifying them of a business start up is a different type of action to completing self assessment forms which are relevant only after your business has been trading. If you have only recently started your business, there will not be any tax due yet so no need to start worrying if you are having problems finding your way around their forms.
When it comes to completing forms online for your tax assessment, you will need to complete separate forms for each paid employment that you have (working for an employer) and also to complete separate forms for each business that you run as a self employed person.
Somewhere at the beginning of the online form completion process, the tax office system should give you the option of saying how many paid employments you have and how many self employments you have, and the system will then generate additional online forms for you to complete as are needed.
If you cannot get the online forms working correctly for you, please read the relevant guidance notes on the HMRC website which should explain everything for you.
http://www.hmrc.gov.uk/selfemployed/