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I have a desktop version of my site using yourwebsite.com and a mobile version using m.yourwebsite.com.

Should I treat them as one site and only submit the desktop version along with its sitemap and preferred URL (www.yourwebsite.com / yourwebsite.com) to search engines, and what what is the right way to use the robots.txt and .htaccess file for each site? One for both or each site has their own files?

Does any of this harm search engine visibility, web crawling and SEO ranking or does it make any difference either way?

As of now, I am using the robot.text from the desktop version for the mobile version and redirecting mobile users.

Any suggestions would be appreciative.

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Should I treat them as one site and only submit the desktop version

They are essentially 2 different sites. Both should have their own robots.txt, sitemaps and URLS (m.yoursite.com and yoursite.com) crawled and submitted for index to Google. As for Yahoo and Bing. Submitting to one essentials submits to both, and honestly I do not focus on them too much. Make sure you are good with Google, or you will suffer.

In regards to both domain names crawled and indexed, bots know the difference and it will not be considered duplicate content. In fact, if you do not have a crawled mobile site and use both domains, that will hurt your rankings. Responsive designs do not require this method.

If you have not yet, go sign up for Google Webmaster Tools, and add your website name, both URL variations along with a sitemap for both. Do this after you take care of the following. (Learn how to setup Google Webmaster Tools)

As stated on Google's Developers Website - Mobile Friendly Websites

Common mistakes

This page describes some of the most common mistakes webmasters make when designing for mobile.

Blocked JavaScript, CSS, and Image Files

For optimal rendering and indexing, always allow Googlebot access to the JavaScript, CSS, and image files used by your website so that Googlebot can see your site like an average user. If your site’s robots.txt file disallows crawling of these assets, it directly harms how well our algorithms render and index your content. This can result in suboptimal rankings.

Recommended actions:

  1. Make sure that Googlebot can crawl your JavaScript, CSS and image files by using the "Fetch as Google" feature in Google Search Console. It will allow you to see exactly how Googlebot sees and renders your content, and it will help you identify and fix a number of indexing issues on your site.

  2. Check and test your robots.txt in Google Search Console.

  3. Test your mobile pages with the Mobile-Friendly Test to see if our systems detect your website as compatible for mobile users.

  4. If you use separate URLs for your mobile pages, make sure to test both the mobile and the desktop URLs, so you can confirm that the redirect is recognized and crawlable.

Also, make sure your mobile site redirect is indeed working by Google's standard, which is explained with a mobile friendly checker on the link provided above.

There are a few ways to achieve this and 2 of them being as follows.

.htaccess file method

 RewriteEngine On
 # Check for mime types commonly accepted by mobile devices
 RewriteCond %{HTTP_ACCEPT} "text\/vnd\.wap\.wml|application\/vnd\.wap\.xhtml\+xml" [NC]
 RewriteCond %{REQUEST_URI} ^/$
 RewriteRule ^ http://m.domain.com%{REQUEST_URI} [R,L]

Javascript Method:

<script type="text/javascript">
  <!--
  if (screen.width <= 800) {
  window.location = "http://m.domain.com";
  }
  //-->
</script>
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Should I treat them as one site and only submit the desktop version along with its sitemap and preferred URL (www.yourwebsite.com / yourwebsite.com) to search engines.

No, you should submit all of the property in search console, and that's how you can track your ranking individually, so submit all the version of website, like www.example.com, example.com and m.example.com

and what what is the right way to use the robots.txt and .htaccess file for each site? One for both or each site has their own files?

Your all of property should have different sitemap and robots.txt, like

www.example.com/robots.txt
m.example.com/robots.txt
www.example.com/sitemap.xml
m.example.com/sitemap.xml 

For redirection, you have many option for redirection, personally most of big website like Google and Facebook use browser useragent and device size for redirection.

Does any of this harm search engine visibility, web crawling and SEO ranking or does it make any difference either way?

Yes, checkout this guideline

  1. On the desktop page, add a special link rel=”alternate” tag pointing to the corresponding mobile URL. This helps Googlebot discover the location of your site’s mobile pages.
  2. On the mobile page, add a link rel=”canonical” tag pointing to the corresponding desktop URL.

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