Assuming you have amd64 architecture because I don't know what you have, read
Then edit the /etc/portage/package.use
media-sound/amarok -kde -accessibility debug
(just an example, change yours)
Then emerge -pv amarok again, and it should show those changes. If you need more changes, go back and edit /etc/portage/package.use again.
emerge -av media-sound/amarok
The USE="some_flag" emerge amarok is a bad idea.
Editing the package.use file will insure that future upgrades of the software still have the same USE flags. package.use will override the settings only for specified flags of an individual package, override the ones from make.conf and the ones set by default (the defaults are set depending on which eselect profile set you used).