Ok. Working with HABTM table. Payment Transactions belong to many Invoices. But trying to assign the association between a single payment and multiple invoices using the link() function doesn't seem to be working. Here is my code:

payment-association.php

    /*
     * Apply Payments to Invoices
     */
    public function applyPayments() {
    	$this->loadModel('PaymentMethods');
    	
    	$invoices	= $this->Invoices
        	->find( 'summary' )
        	->where([ 'Invoices.id IN' => $this->request->data( 'invoices' ) ]);
        // Add totals:
        $totals	= $this->InvoiceTotals->doTotals( $invoices );
        extract( $totals );
        
        $payment_methods	= $this->PaymentMethods->find('list', [
			'keyField' => 'shortname',
			'valueField' => 'name'
        ]);
        
        if ( $this->request->data( 'apply_payment' ) ) {
			$payment	= $this->Invoices->PaymentTransactions->newEntity();
			$payment	= $this->Invoices->PaymentTransactions->patchEntity( $payment, $this->request->data );
			if( $new = $this->Invoices->PaymentTransactions->save($payment) ) {
				// die( print_r( $invoices ) );
				$invoices->each( function( $invoice, $key ) use ( $new ) {
					$this->Invoices->PaymentTransactions->link( $invoice, [$new] );
				} );
				$this->Flash->success(__('The payment has been saved.'));
				$this->set( 'new', $new->id );
				// return $this->redirect(['action' => 'applyPayments', $new->id]);
			} else {
				$this->Flash->error(__('The invoice could not be saved. Please, try again.'));
			}
        }
    	
    	$incoming	= $this->request->data( 'invoices' );
    	$this->set( compact( 'incoming', 'invoices', 'batch', 'payment_methods' ) );
    	$this->viewBuilder()->layout('partial');
    }