서버 Apache/2.0.55 (Ubuntu) 입니다.

/etc/apache2/apache2.conf 에 httpd.conf,port.conf등을 인클루드하는 형태로 설정을 잡더군요.

질문의 요지는 하나의 ip:80 포트만 사용하여 두개의 도메인을 각각 다른 경로에 세팅해주는 방법입니다.

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설정 파일가운데 호스트 관련 부분은 아래 내용이 전부입니다.
/etc/apache2/sites-available/default

NameVirtualHost *
<VirtualHost *>
ServerAdmin master@gaetgol.net
DocumentRoot /home
#SerName gaetgol.net
#ServerAlias www.gaetgol.net
<Directory />
Options FollowSymLinks
AllowOverride None
</Directory>
<Directory /home>
Options Indexes FollowSymLinks MultiViews
AllowOverride None
Order allow,deny
allow from all
# Uncomment this directive is you want to see apache2's
# default start page (in /apache2-default) when you go to /
#RedirectMatch ^/$ /apache2-default/
</Directory>

ScriptAlias /cgi-bin/ /usr/lib/cgi-bin/
<Directory "/usr/lib/cgi-bin">
AllowOverride None
Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
Order allow,deny
Allow from all
</Directory>

ErrorLog /var/log/apache2/error.log

# Possible values include: debug, info, notice, warn, error, crit,
# alert, emerg.
LogLevel warn

CustomLog /var/log/apache2/access.log combined
ServerSignature On

Alias /doc/ "/usr/share/doc/"
<Directory "/usr/share/doc/">
Options Indexes MultiViews FollowSymLinks
AllowOverride None
Order deny,allow
Deny from all
Allow from 127.0.0.0/255.0.0.0 ::1/128
</Directory>

</VirtualHost>

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# 사용자 디렉토리
/etc/apache2/mods-enabled/userdir.conf

<IfModule mod_userdir.c>
UserDir www
UserDir disabled root

<Directory /home/*/www>
AllowOverride FileInfo AuthConfig Limit
Options MultiViews Indexes SymLinksIfOwnerMatch IncludesNoExec
</Directory>
</IfModule>