// Get the movie for the show we try to add from array of all movies
$movieEntry = $movies[$showEntry->movieID];

// Get the currently listed shows from the movie
$movieEntryShows = $movieEntry->shows->ids();
// Add show if not already there
if ( !in_array( $showEntry->id, $movieEntryShows ) ) {
  array_push( $movieEntryShows, $showEntry->id );
}

// Set updated list of shows back to the movie
$movieEntry->setContentFromPost(['shows' => $movieEntryShows]);

// Save movie
$success = craft()->entries->saveEntry($movieEntry);

$test = ['1288', '1299', '1291'];
$movieEntry->setContentFromPost(['shows' => $test]);
$success = craft()->entries->saveEntry($movieEntry);