I was getting crazy trying to solve this. Finally I found the solution.

After create the X Websites you need from your Admin section we hace to edit a piece of code.

Note: each Website has one unique Store and one unique Store View.
Note2: use short and easy Websites codes, we will need them now.

Sub Domain Method

In your Index.php file (in the root directory of the Magento installation) you have to look for:
$mageRunCode = isset($_SERVER[‘MAGE_RUN_CODE’]) ? $_SERVER[‘MAGE_RUN_CODE’] : ”;

$mageRunType = isset($_SERVER[‘MAGE_RUN_TYPE’]) ? $_SERVER[‘MAGE_RUN_TYPE’] : ‘store’;

Mage::run($mageRunCode, $mageRunType);

Then replace the found code for this new one:
// this first line detects the domain / sub domain
switch($_SERVER[‘HTTP_HOST’]) {

case ‘store1.domain.com’:

/* store1 is the code you wrote in the admin
when created the website */
Mage::run(‘store1’, ‘website’);

break;

// domain.com (default store)

default:
Mage::run();

break;

}
Sub Directory Method

Using a Sub Directory means more job.

First of all you need to create as much as directories you wanna have.

Example:

    http://mydomain.com/store1
    http://mydomain.com/store2

So following the example you will create 2 directories in the root of your magento installation.

Now you have to copy & paste the index.php and the .htaccess to those folders.

Once that we need to edit the index.php.

Look for:
$mageRunCode = isset($_SERVER[‘MAGE_RUN_CODE’]) ? $_SERVER[‘MAGE_RUN_CODE’] : ”;

$mageRunType = isset($_SERVER[‘MAGE_RUN_TYPE’]) ? $_SERVER[‘MAGE_RUN_TYPE’] : ‘store’;

Mage::run($mageRunCode, $mageRunType);

And replace it for:
// this will force to load the Website with the code store1
Mage::run(‘store1’, ‘website’);

You need to repeat this step to every folder, to every index.php you created before.

Now check out this screenshot to see how to configure the Website:

Done!

Now you know how to create multiples Websites in one Magento Installation.