I see you switched the two variables I might have been unclear. I meant the following:
<VirtualHost *:80>
DocumentRoot /var/www/html
ServerName exampleone.com
SetEnv MAGE_RUN_TYPE "website"
SetEnv MAGE_RUN_CODE "exampleone"
</VirtualHost>
If it might help someone …
The way I am using this on Nexcess is by adding the second domain as a pointer and add this on top of my .htaccess
file in my html root directory:
SetEnvIf Host .*exampleone\.com.* MAGE_RUN_TYPE=website
SetEnvIf Host .*exampleone\.com.* MAGE_RUN_CODE=exampleone
SetEnvIf Host .*exampletwo\.com.* MAGE_RUN_TYPE=website
SetEnvIf Host .*exampletwo\.com.* MAGE_RUN_CODE=exampletwo