The code for creating the Household Account is completed by the Nonprofit Starter Pack. We create Contact with Account blank and NPSP assigns household account. 

The contact should be setup correctly with the household account. However, the Payment Txn will not have an account linked to it. If you want to have Account linked then you can may be create a process  on Payment Txn object ( Please be careful while using Process builder as it can break things. use criteria Status- "Receipting Complete")