If you wish to be able to control all domain on an account before they resolve, you can do so by creating some symbolic links. Lets say you have domain1.com and domain2.com which you want to be able to access. You'd run the following as the user through ssh:
cd /home/username
rm -f public_html
mkdir --mode=755 public_html
cd public_html
ln -s ../domains/domain1.com/public_html domain1.com
ln -s ../domains/domain2.com/public_html domain2.com

Alternatively, if you just wish to switch which domain is being used for /~username, you can do so by loggin into the User Panel -> Domain Administration -> select the active domain to use and click "Set as Default". This will setup the symbolic link for the selected domain for /~username.

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