Add posts to WP Query object

You can modify the query using the pre_get_posts hook, you will have to add the parameters of your query to the query provided by WordPress inside you callback function (exclude_category in the example below):

Example from the WordPress Codex:

function exclude_category( $query ) {
    if ( $query->is_home() && $query->is_main_query() ) {
        $query->set( 'cat', '-1,-1347' );
    }
}
add_action( 'pre_get_posts', 'exclude_category' );