Just visit KRA offices, request for a ledger balance of your PIN from where your have been registered (your station) e.g. North of Nairobi is 14th Floor, East is 17th Floor and South is Wilson Airport, West is Forodha Community.
Take your statement you simply pay the amount at the bank, with attached VAT 28 Forms (for penalties) preferably National Bank, Coo-op or KCB and pay to Commissioner of Domestic Taxes. After payment you can apply for your tax compliance certificate...