Apache running on Yosemite not working as expected
You've essentially set up two different sites here:

For http://localhost your files are stored in /Library/Webserver/Documents.

For http://localhost/~username the files are stored in ~username/Sites

Therefore, anything you put in ~username/Sites will only be available when you go to http://localhost/~username.  If you want to keep the two things separate, you'll need to put the "phpmyadmin" under /Library/Webserver/Documents instead of http://localhost/~username.