wp_insert_post.php

<?php
global $wpdb;

// Insert the original post
$original = wp_insert_post($array, true);

// Insert the translated post
$translated = wp_insert_post($array, true);

// Make some updates to both translations
update_post_meta();
wp_set_object_terms();
// ... and so on

// Associate translated language and original language
$trid = wpml_get_content_trid('post_<your_custom_post_type>', $original );
$wpdb->update( $wpdb->prefix.'icl_translations', array( 'trid' => $trid, 'language_code' => '<your_language_code>', 'source_language_code' => wpml_get_default_language() ), array( 'element_id' => $translated ) );

// That's it