I think pay now should be adjusted to the following formula: pay now = due to date - payments & credits. So it'd break down like this:
a $3,000 balance split into three payments
$1,000 due October 1 Due to date October 1 - $1,000
$1,000 due November 1 Due to date November 1 - $2,000
Balance due December 1 Due to date December 1 - $3,000
So, if they paid $750 by October 1 they would be assessed a late fee for not making the first payment in full and the pay now about for November 1 would $2,000 (due to date) - $750 (actual payments) = $1,250. Does that make sense? Let me know what you think.