Payment Entry or Journal Entry?

It can: a Journal Entry row can carry a party. A Payment Entry is the better habit, because it links to the invoice, handles deductions and feeds Payment Reconciliation cleanly.

When the money moves through a bank account, a Payment Entry needs a Reference No and Reference Date. That is what bank reconciliation matches against later.

For Receive and Pay, yes: a customer, supplier, employee or shareholder. An Internal Transfer between your own bank and cash accounts needs none.

From Frappe HR, a separate app. Its payroll creates the accounting entries, so they are not raised by hand.