This doesn't seem to be true in my experience. I have invoices with multiple items and each item has a different sub-class assigned to it.

If I enter a partial payment, that payment somehow gets spread, seemingly randomly, over the different items. I can see this fact on the Balance Sheet By Class report. 

Example: Invoice total is for $74921.33 split amongst sub-classes as follows: 

$67,745.30

$365.00

$6,811.03

I apply a payment of $1,150.22 to that invoice. On the Balance Sheet By Class it shows the following amounts as "Undeposited Funds":

$1040.05

$5.60

$104.57

with a total "Undeposited Funds" of $1150.22

So how do you explain that? And how does it decide how much to apply to each sub-class? It appears to do it by percentage. For example, the $6811.03 sub-class is 9.09% of the total invoice and it's corresponding payment amount of $104.57, which is about 9.09% of the payment amount of $1150.22.

So this is not true: "In QuickBooks, payments are applied to the overall total of an invoice, not per line item."

Rick