When I create a bill relating to cis sub contractor it goes into the expenses as an expense. Then when I pay it, it appears as a bill payment as a minus.

when you enter a bill and use the expense account, that is fine

but having used enter bills, you have to use pay bills to associate the payment with the bill, when you make that payment you are paying accounts payable so you do not also put an expense account on the payment - and of course you make the payment using a bank account or credit card