The loan is repaid automatically - when the installment is paid you hear a sound of an opening cash desk and appropriate information is displayed in lower right corner (at the bottom of Route Advisor). If you have a loan the installments are paid everyday at the time of taking it. If you have more loans all the installments are paid at noon.
You can check the number of paid installments in the bank window. You can repay the whole loan by clicking on "Repay loan" button. You cannot repay its remaining part - either you pay the whole sum or you pay in installments.