To rephrase, I believe what you're asking is how can you have a different style or template for your custom post types when they are displaying as a list?
It looks like the Custom Post Templates plugin you're using only allows you to switch templates for the single view of a post, not the listing of the posts, which is what I think you mean when you say index?
If you just need a way to style your posts separately, this depends on your theme, but in TwentyTwelve and TwentyThirteen, in index.php, it has the loops that, if posts exists, displays them, or displays a message if there are no posts. If you just need a class to use so that you can style each post type's archive separately, you can use a PHP if statement to check for your custom post type and add a class if it's true. Here's an example. Let's say my custom post type is called recipe_posts, and I want to add a class called "recipe-archive" for when those posts are being displayed in list form, I would write something like this in TwentyThirteen's index.php:
<div id="primary" class="content-area <?php if(get_post_type() == recipe_posts): ?>recipes-archive<?php endif; ?>">
<div id="content" class="site-content" role="main">
<?php if ( have_posts() ) : ?>
<?php /* The loop */ ?>
<?php while ( have_posts() ) : the_post(); ?>
<?php get_template_part( 'content', get_post_format() ); ?>
<?php endwhile; ?>
<?php twentythirteen_paging_nav(); ?>
<?php else : ?>
<?php get_template_part( 'content', 'none' ); ?>
<?php endif; ?>
</div><!-- #content -->
</div><!-- #primary -->
Here I added a class to where "content-area" is with
<?php if(get_post_type() == recipe_posts): ?>recipes-archive<?php endif; ?> but really, you can use this method where you need it to make styling easier. Now if you want to change templates, by default, in TwentyTwelve/Thirteen, it uses content.php that gets called in index.php. You can use the same PHP if statement if you want to swap out
<?php get_template_part(); ?> with something else.
Hope that helps. Good luck!