Hi arapaoakiwi
What are the wage expense accounts you have and are there used on an employee all the time or just for a specific role they may be doing at the time?
ie if you have on site wages and say factory wages then you should have two pay items set up. One of the you would just leave as going to the default wages account (say on site) and then other one you set up would be called Factory wages, and when creating that category you tick the box 'override employees wage expense account and choose the expense account you want it to go to.
If you have set up jobs then when processing the pay run you should be able to choose the job.
This can not be done after the payrun has been processed though.
If you wanted to adjust for pays already done and unallocted you would pass a general journal entry, crediting the wage expense account with the gross wage expense and super accounts and allocated to no job, then debit the same amount to both those accounts with a job allocated.
This will leave the super and wage expense the same but allocate them to the job in question.