Hi Authority Sitebuilder, First of all Google doesn't seem to care about these but for users' sake, for the sake of conformity and as a good practice, it is best to do a redirect

from(example)

http://www.website.com

to

http://www.website.com/index.php

In other words, select one URL and stick with it, redirect all others. Make a 301 redirect of your old URLs to your new URLs. Then it should not affect your ranking unless you will do some other changes on your pages As you said earlier that all the back links go to the  http://www.website.com (old url), so it is better to redirects o the new url i.e  http://www.website.com/index.php

I hope that your query had been solved.

Hi KS_,

As you know that Directory submission mostly used by all the business companies for the promotion of their websites or products.

The directory & classified submissions are mainly used for getting listing in all major & useful directories.

The both above submissions are used according to the target area or population.Classified submissions are similar to yellow pages.The most important  thing to remember while doing listing is that it should be of same niche where the listing is to be done. This will leads to indexed pages & rank higher in search engines & it will helps to gain visibility via search engines.

The above both submission helps to increase in sales of products, website presence specially in search engines.These will helps to gain non reciprocal back links from high Page Rank Websites/ Directories.

I hope that your query had been solved.