This has been a real bug bear for me for many years as I controlled a payroll company with over 300 employees and which generated a lot of employee liabilities to acquit.
One of the first methods I adopted was to :
1. Set a shorter date period - e.g. 1st to 7th Oct 2012 = $5,456.00
rather than opting for the full month e.g. 1st to 31st Oct = $21,369.00
I still ensure that all the appropriate memos are included including the dates and don't forget to insert the ATO as the "supplier"
The other method I have had to adopt was caused when other users simply made a bulk payment without even checking with me as to the amount of the month's liability (the boss). In these cases, I made the "bogus" payment from a newly created bank clearing account and when making the various installments to make up the total, these were coded back to the same clearing account. Over time, the amount/s paid should equal the amount of the month's liability.
I hope this helps
Greg