If you just want to change the options to the configure script then, change them in debian/rules and to change the version number (I'm not 100% on this) you should just add an entry to the top of debian/changelog
Then just do (from the top of the source dir:
(configures and runs make)...
user@host:ethereal-0.99.0$ fakeroot debian/rules binary
if you don't have fakeroot installed use sudo
then you should have the debs in the directory above the source.