htaccess issue with URL masking

Question

I am attempting to mask an URL using an htaccess file to only show the root URL. This is a Drupal 7 website, so I want the URLs to look like the following:

Main page:
  http://www.site1.com
Drupal content:
  http://www.site1.com/content/....

There is also a test site that should appear as:

Test site:
  http://www.site1.com/site1-test
Test content:
  http://www.site1.com/site1-test/content/...

The directory structure is as follows:

 public_html/
            |--site1/
            |--site1-test/

Here is the htaccess file I've been working on in public_html/.htaccess. It mainly works, however there is a small issue. When I visit site1.com the URL appears as I want, however whenever I click any content it shows site1.com/site1/... instead of hiding the extra subdirectory. This is based on a prior StackOverflow question.

public_html/.htaccess

Options +FollowSymLinks
RewriteEngine on
#========================================================================
# FIRST Handle the http requests first before removing the additional url junk
#========================================================================
RewriteCond %{HTTP_HOST} ^(www.)?site1.com$
RewriteCond %{REQUEST_URI} !^/site1/
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ /site1/$1

RewriteCond %{HTTP_HOST} ^(www.)?site1.com/site1-test$
RewriteCond %{REQUEST_URI} !^/site1-test/
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ /site1-test/$1

#==========================================================
# SECOND Remove the additional url junk once the new url is loaded
#==========================================================
RewriteCond %{HTTP_HOST} ^(www.)?site1.com$
RewriteRule ^(/)?$ site1/index.php

RewriteCond %{HTTP_HOST} ^(www.)?rg$
RewriteRule ^(/)?$ site1/index.php

Previously I'd updated the $base_url variable in the settings.php file, however that seemed to break my themes unless if I pointed it directly to site1.com/site1, rather than to site1. At present, there is no defined $base_url.