I too ( and many other users, I'll bet) have same issues with dysfunctional/unusable QBO "features". 

Cleverly disguised and misrepresented as helpful tool, QBP payment links and online invoice payments do NOT attach/post or in any way record to actual invoices.  Seems like ALL payments apply as lump sum balance. Seriously? Unbelievable! What accounting or intelligent bookkeeper would design system this way?

So if online payment links are sent to client and they pay, even if invoices are shown in payment portal prior to payment, the funds do not auto attach to specific invoices.   Worse, send payment request with a flat amount QB automatically creates a sales receipt for that amount when YOU ALREADY HAVE INVOICES WAITING.  Workaround..  delete sales receipt then apply payments manually through deposit, otherwise you end up with double expensed items.   WT?!?!?   

If you try enabling auto apply credits in settings (thinking vendor credits) be prepared for incoherent, overpriced QB to then randomly apply client payments anywhere for that client, resulting in tons of partial payments all over the place. 

Neither options provide clarity for clients or frustrated QBO users.

That QB defaults to these barely>non-functional settings and lack of options is ridiculous.  Emailed emailed notifications from QBP/QBO web version do NOT offer any invoice/payment detail via reports, QBP useless portal or within QB or anywhere.  However, alerts from QB mobile app notifies of exact payment, client/payee AND WHICH ITEM WAS PAID.    Basic functionality does not exist for QBO