If your port needs to build slightly different versions of packages by having a variable (for instance, resolution, or paper size) take different values, create one subdirectory per package to make it easier for users to see what to do, but try to share as many files as possible between ports. Typically you only need a very short Makefile in all but one of the directories if you use variables cleverly. In the sole Makefile, you can use MASTERDIR to specify the directory where the rest of the files are. Also, use a variable as part of PKGNAMESUFFIX so the packages will have different names.
This will be best demonstrated by an example. This is part of japanese/xdvi300/Makefile;
PORTNAME= xdvi
PORTVERSION= 17
PKGNAMEPREFIX= ja-
PKGNAMESUFFIX= ${RESOLUTION}
:
# default
RESOLUTION?= 300
.if ${RESOLUTION} != 118 && ${RESOLUTION} != 240 && \
${RESOLUTION} != 300 && ${RESOLUTION} != 400
@${ECHO} "Error: invalid value for RESOLUTION: \"${RESOLUTION}\""
@${ECHO} "Possible values are: 118, 240, 300 (default) and 400."
@${FALSE}
.endif
japanese/xdvi300 also has all the regular patches, package files, etc. If you type make there, it will take the default value for the resolution (300) and build the port normally.
As for other resolutions, this is the entire xdvi118/Makefile:
RESOLUTION= 118
MASTERDIR= ${.CURDIR}/../xdvi300
.include "${MASTERDIR}/Makefile"
(xdvi240/Makefile and xdvi400/Makefile are similar). The MASTERDIR definition tells bsd.port.mk that the regular set of subdirectories like FILESDIR and SCRIPTDIR are to be found under xdvi300. The RESOLUTION=118 line will override the RESOLUTION=300 line in xdvi300/Makefile and the port will be built with resolution set to 118.