Apache running on Yosemite not working as expected I plan to use both /Library/Webserver/Documents and ~username/Sites/. I have phpmyadmin folder in /Sites directory. If I go to 

http://localhost/~username/phpmyadmin


it works, but if I go to

http://localhost/phpmyadmin 


I get "The requested URL /phpmyadmin/ was not found on this server.". I've reviewed the relevant files to make sure I enabled the relevant lines and such. Am I missing something obvious?
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.