I followed the following basic steps:

USE="vhosts" emerge -p awstats
Remove -p pretend after you've seen what dependancies are required.

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Create conf file:
ln -s /usr/share/webapps/awstats/6.9-r1/postinst-en.txt /etc/apache2/vhosts.d/awstats.conf

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Edit the apache conf file:
nano /home/dev/apache/conf/vhosts.conf

Add something similar like this, changing the default location of awstats for security. Further access restrictions are set below:

ScriptAlias /pkd-stats "/usr/share/webapps/awstats/6.9-r1/hostroot/cgi-bin/"
Alias /pkd-stats-icons "/usr/share/webapps/awstats/6.9-r1/htdocs/icon/"

<Directory /usr/share/webapps/awstats/6.9-r1/hostroot/cgi-bin/>
        Options +ExecCGI +FollowSymLinks
        AllowOverride None
        Order allow,deny
        Allow from all
</Directory>

<Directory /usr/share/webapps/awstats/6.9-r1/htdocs/icon/>
        Options +ExecCGI +FollowSymLinks
        AllowOverride None
        Order allow,deny
        Allow from all
</Directory>

CustomLog "|/usr/sbin/cronolog /home/dev/apache/logs/tcs-%Y-%m-%d.log" combined

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Duplicate the config file creating a new for the domain that your running and edit:

cd /etc/awstats/
cp awstats.module.conf awstats.www.pkdavies.com.conf
nano /etc/awstats/awstats.www.pkdavies.com.conf

Set the following:
LogFile="/usr/bin/logresolvemerge.pl /home/dev/apache/logs/pkd-*.log |"
SiteDomain="www.pkdavies.com"
DNSLookup=1
DirCgi="/pkd-stats"
DirIcons="/pkd-stats-icons"
AllowFullYearView=3
AllowToUpdateStatsFromBrowser=1
SkipHosts="127.0.0.1 REGEX[^192\.168\.] REGEX[^10\.]"

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Change the owner of the files:

cd /usr/share/webapps/awstats/6.9-r1/hostroot
chown -R apache:apache datadir
chown -R apache:apache cgi-bin

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Now update the stats from existing log files
perl awstats.pl -config=www.pkdavies.com -update

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Now password protect the access.
Create the password file (replace the word username & password with anything you like)

htpasswd -bc /etc/awstats/.htpasswd username password

In my case it involved editing the main httpd.conf file and adding the awstats.conf file uncommenting:

<Location "/pkd-stats/awstats.pl">
    AuthType Basic
    AuthName "AWStats authenticated zone"
    AuthUserFile /etc/awstats/.htpasswd
    Require valid-user
</Location>

Reload Apache
apache2ctl configtest
apache2ctl graceful