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 If you still have ports installed you might wanna move them out of the way. 
/usr/local
/usr/X11R6
/var/db/pkg

To make cvs work sanely, add this to your ~/.cvsrc files: 
 cvs -z4 -q
 diff -u -p -N
 update -dP
 checkout -P

In the default pkgsrc will have its makefiles under /usr/pksrc and install to /usr/pkg and its DB of installed packages in /var/db/pkg, pkgsrc-wip makefiles are under /usr/pkgsrc/wip. 
Fetch a snapshot of pkgsrc (ftp://ftp.netbsd.org/pub/NetBSD/packages/pkgsrc-current.tar.gz) and pkgsrc-wip (http://pkgsrc-wip.sourceforge.net/snapshots/) (wip = work in progress). Unpack them: 
cd /usr
bsdtar xf .../pkgsrc.tar.gz
cd pkgsrc
cvs up
bsdtar xf .../pkgsrc-wip....tar.gz
cd wip
cvs up

Bootstrap pkgsrc: 
cd /usr/pkgsrc/bootstrap
./bootstrap
mkdir /usr/pkg/etc
cp work/mk.conf.example /usr/pkg/etc/mk.conf

Add /usr/pkg/bin and maybe /usr/pkg/sbin to your $PATH or symlink /usr/local /usr/pkg: 
cd /usr
ln -sf pkg local

Install pkgmanager:
cd /usr/pkgsrc/wip/pkgmanager
bmake install