Debian-apache uses dpatch to make changes to the upstream source.

To apply all of the patches run:
./debian/rules patch

To unapply all of the patches run:
./debian/rules unpatch

To add (or edit) a patch run:
dpatch-edit-patch name_of_patch_goes_here
#make your changes
exit

dpatch will make a new patch in debian/patches/ if one with that name doesn't already exist, otherwise it will change the existing one.
To make it get used add it to debian/patches/00list .

To make a patch not get used remove it from debian/patches/00list .