The best thing would be to convince upstream to Do The Right Thing(tm). Meanwhile, you can add stuff like this to your install target in debian/rules:
DMANDIR=$(CURDIR)/debian/foobar/usr/share/man
install: build-stamp
....
${MAKE} install DESTDIR=$(CURDIR)/debian/foobar
mv ${DMANDIR}/man1/thisbelongsto5.1 \
${DMANDIR}/man5/thisbelongsto5.5
...
Not the nicest, but works. If you have lots of manual pages to move,
you might want to store them in a variable, and do a for loop or
something.
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