Use flags can be set in different ways :

 1. By using the env variable

  example:

localhost ~ # USE="-debug doc" emerge apache

 2. By modifying the /etc/portage/package.use file

 3. By modifying the /etc/make.conf file

 4. By modifying the make.defaults file from your profile

Note: Pay attention to the order these ways are set; it reflect the prior order of the use declaration. (first is the strongest)

Use flags available /usr/portage/profiles/use.desc

Local Use flags available /usr/portage/profiles/use.local.desc