I have also had the same issue, changed from one accounting software to another and had quickbooks set up by professional however now i have 80% doubled up payments on invoices.  Expenses that dont even show up in accounts and a BAS that looks like i should sell my car to pay for. Payments in my news feed that dont marry up with any invoices as all, let alone are even present on my bank statement.  Its a complete mess of false numbers.

One step at a time....

How do i remove odd payments?

then 

How do i create a report that only shows what i need to manually check off my bankstatement against invoices raised and paid in period.

How do i create a report to only show what i need to manually check off my bankstatement against expenses paid.

thanks