There is a good guide how to make custom login here https://www.drupal.org/node/350634
But to make some advanced changes I created this overrides. I repositioned the links below the submit button with deleting the array values and then adding it to the end of form array. Also I changed the text of the links to register and reset password
function mytheme_preprocess_user_login(&$vars) {
$items = array();
$items[] = 'Not registred yet? '.l(t('Sign up here!'), "user/register", array('attributes' => array('title' => t('Create a new user account.'),'class'=>'register')));
$items[] = l(t('Request new password'), 'user/password', array('attributes' => array('title' => t('Request new password via e-mail.'),'class'=>'register')));
$vars['form']['links']['#markup'] = theme('item_list', array('items' => $items));
$temp = $vars['form']['links'];
unset($vars['form']['links']);
$vars['form'][] = $temp;
}