The following is an old FAQ which has been officially removed for a long time.
I want to perform the ./configure step myself. Can I?
Yes, but it is not trivial, and the next method only works when it is a simple ebuild (i.e. just ./configure and make && make install). Be sure to read the ebuild itself to see how Gentoo handles it.
Start with unpacking the ebuild: ebuild /usr/portage/<category>/<package>/<ebuild> unpack.
Next, go to /var/tmp/portage/<package>-<version>/work. Inside it you'll find the unpacked sources. Execute the steps you need to perform to configure and compile the package.
When finished, execute touch /var/tmp/portage/<package>-<version>/.compiled to trick Portage into thinking it configured and compiled the package. Then finish up with ebuild /usr/portage/<category>/<package>/<ebuild> merge.