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Subdomain versus subdirectory

We have two sites, one is mainly a portfolio site (built with Yii framework) and the other is a digital shop (built with open cart) where we sell plugins and themes. The url's look like www.mydomian.com and www.store.mydomain.com. But of these sites are in the same server. We use google analytics tools and have no problem getting traffic to our store. But we have very little to our portfolio site and we want to increase our Google ranking for this site. Assuming increased traffic to our site will increase our google ranking, we were thinking to use URl masking so the link will be www.mydomain.com/shop and this will load www.store.mydomain.com. Will this count as hits for our portfolio site? Because the .htaccess rules will ensure the subdomain is served. So I dont know if these hits will count on our store or our portfolio site...