You do include VAT in your cost of sales figure and for any other expenses business expenses you pay VAT on. You add the non CIS income to the CIS income if it is the same business. For instance, I have clients who do CIS work as electricians and have 20% tax deducted. They also do work in people's homes and obviously no tax is deducted from their earnings for those jobs. However, all the earnings are combined and disclosed in the same set of self-employment pages.
Was all your work income from doing the same type of work? If it was you add it all up and show it in the turnover box of the self-employment pages I gave you a link to earlier on. The fact that some had tax deducted and some didn't doesn't matter.
Where you have had tax deducted you use the pre-tax figure. You add that to the income where no tax has been deducted and that is your income before expenses. The 20% tax that you have suffered on some of the income will be shown as a deduction from your tax liability at the bottom of the tax calculation which you can see if you click on "View my calculation".I'm not sure what you mean by "should of paid 20%.". If you work on a construction site for a main contractor they will deduct 20% tax if you are registered within the CIS system run by the tax office. If you work at a private individual's house building a wall, they won't deduct tax because they are not part of the CIS system. All you need to do is declare all your income and not worry about what other people should have done as far as deducting tax is concerned.I'm assuming you are registered within the CIS system as you have paid 20% tax on some of your income. If you were not registered, you would be having 30% tax taken off. Read about the CIS scheme here.
Nothing. You simply declare all your income and pay any tax due. As I said before, work you do on somebody's house for example will not be covered by the CIS scheme.