Payroll was entered manual and now entering in module -- Different amounts

Taking over a client who entered payroll in GJ from the online CRA payroll calculator.  The journal entries have wrong calculations (for income tax) and one employee was CPP maxed but she continued to post/deduct.  When I am re-entering the information (in the payroll module from the GJ) how is this best handled?  The cheque net amount has to line up with the bank, the source deduction amounts that have been submitted are incorrect, the T4's are effected (how to post to ensure correct).