wordpress post query loop config

I’m new to loop customisation and I have an issue getting my search page front end filter loop working in the same way as my other category template post loop.

This is the loop I am using for the category templates which works fine.

<?php $custom_query_args = array( 'cat' => '2', 'posts_per_page' => 6 );
          $custom_query_args['paged'] = get_query_var( 'paged' ) ? get_query_var( 'paged' ) : 1;
          $custom_query = new WP_Query( $custom_query_args );
          $temp_query = $wp_query;
          $wp_query = NULL;
          $wp_query = $custom_query;
          if ( $custom_query->have_posts() ) :
          while ( $custom_query->have_posts() ) :
          $custom_query->the_post(); ?>

This allows me to paginate through all posts in this category but I need to convert a similar code block on my search page to allow it to do the same, currently the search template code below doesn’t paginate like the above.

<?php wp_reset_postdata();
          global $wp_query;
          $paged = get_query_var( 'paged' ) ? get_query_var( 'paged' ) : 1;
          foreach($_POST['filter_cat'] as $fcat){$fcat_list .= $fcat . ",";}
          query_posts(
            array_merge(
              array( 
                'cat' => $fcat_list,
                'posts_per_page' => 6,
                'paged' => $paged
                       ),
              $wp_query->query
                )
            ); ?>

          <?php if ( have_posts() ) : while ( have_posts() ) : the_post(); ?>

I know that the first code block is a better method but I can’t figure out how to use the second block in the same way.

Edit:

Ok please excuse my inexperience.

Thanks to Pieter Goosen I’m part way there with using pre_get_posts.

I’ve done so successfully with category template but using the following for the search page template kills the site, I’m not sure where I’m going wrong.

function paginate_search ( $query ) {
if( $query->!is_admin() ) {
foreach($_POST['filter_cat'] as $fcat){$fcat_list .= $fcat . ",";}
query_posts( array_merge ( array ( 
                      'cat' => $fcat_list,
                      'posts_per_page' => 6,
                      'paged' => $paged
                       ),
                    $wp_query->query
                ) ); } }
add_action( 'pre_get_posts', 'paginate_search' );