The first way ->
a) menu Accounting/Periodic Processing/Reconcilation/Manual Reconcilation
b) menu Accounting/Payment Follow-up/Reconcile Invoices & Payments (module account_followup must be installed)
The second way -> Customer view -> Jurnals Items -> check selected -> More -> Reconcile Entries
You select entries with the same account number (one debit and one credit). If Credit != Debit you click on button Partial reconcile in next step (or Reconcile with Write-Off if expected is to divide the payment for parts). How to select correct Account number? - this account has ... type = Receivable ... and has checked ... Allow Reconciliation = 1
The third way -> menu Accounting/Bank and Cash/Bank Statements.
Create new bank Statement, insert new payment and reconcile with selected invoices or other entries
The fourth way -> install and use module account_voucher + The first way or/and The second way
PS. Invoice is Paid if all corresponding account move lines are reconciled, see method test_paid() in account_invoice.py