add_action('pre_get_posts','wpse50761_alter_query');
function wpse50761_alter_query($query){

      if( $query->is_main_query() ){
        //Do something to main query
      }
}

if( have_posts() ):
    while( have_posts() ): the_post();
       //The loop
    endwhile;
endif;

$my_secondary_loop = new WP_Query(...);
if( $my_secondary_loop->have_posts() ):
    while( $my_secondary_loop->have_posts() ): $my_secondary_loop->the_post();
       //The secondary loop
    endwhile;
endif;
wp_reset_postdata();

<ul>
<?php
global $post;
$args = array( 'numberposts' => 5, 'offset'=> 1, 'category' => 1 );
$myposts = get_posts( $args );
foreach( $myposts as $post ) :  setup_postdata($post); ?>
    <li><a href="<?php the_permalink(); ?>"><?php the_title(); ?></a></li>
<?php endforeach; wp_reset_postdata(); ?>
</ul>

// ...

global $wp_query;
$wp_query = new WP_Query(array('your query vars here')); // sets the new custom query as a main query

// your custom-post-type loop here

wp_reset_query();

// ...

//unfortunately, "IS_PAGE" condition doesn't work in pre_get_posts (it's WORDPRESS behaviour)
//so you can use `add_filter('posts_where', ....);`    OR   modify  "PAGE" query directly into template file

add_action( 'pre_get_posts', 'myf88' );
function myf88($query) {
    if ( ! is_admin() && $query->is_main_query() )  {
        if (  $query->is_category ) {
            $query->set( 'post_type', array( 'post', 'page', 'my_postType' ) );
            add_filter( 'posts_where' , 'MyFilterFunction_1' ) && $GLOBALS['call_ok']=1;
        }
    }
}
function MyFilterFunction_1($where) {
   return (empty($GLOBALS['call_ok']) || !($GLOBALS['call_ok']=false)  ? $where :  $where . " AND ({$GLOBALS['wpdb']->posts}.post_name NOT LIKE 'Journal%')";
}

if( have_posts() ):
    while( have_posts() ): the_post();
       //The loop
    endwhile;
endif;

function have_posts() {
    global $wp_query;
    return $wp_query->have_posts();
}