I'm sorry, I'm the worst at remembering to log on here. Anyway here's some of the stuff I came across. I'm by no stretch an expert so I don't want to get you into a mess, but this worked for me. First thing I did was follow directions I found on another site to move a bunch of startup scripts. I really only use my DS111 for a webserver and a network drive so I don't need most of the built-in apps. So, I created a new directory "rc.off" at /usr/syno/etc.defaults/. Moved scripts I didn't need from /usr/syno/etc.defaults/rc.d to the new directory, /usr/syno/etc.defaults/rc.off, so they don't start on reboot. Specific to the webserver stuff, I moved S97apache-sys.sh and S97apache-user.sh. So yeah as you mentioned the S97apache-sys.sh script will prevent the admin interface from running. When I need to use it I call it with "/usr/syno/etc.defaults/rc.off/S97apache-sys.sh start" and it will start up like normal, then I stop it again with "stop".
Another thing I changed is that the admin page listens on 5000, but it also redirects port 80 to 5000. That's at the bottom of the conf file at /usr/syno/apache/conf/httpd.conf-sys so I commented that part out.
# <IfDefine REDIRECT_USER>
# Listen DONT start at front
# Listen 80
# <VirtualHost *:80>
# RewriteEngine On
# RewriteRule ^/(.*)$ /usr/syno/synoman/redirect.cgi?5000
I can't think of many other problems I ran into. (Aside from getting the webservers themselves running like I wanted.) The ipkg webservers will use the built-in MYSQL, or you can install the ipkg version which uses less memory on mine. (But it's version 4.) You could also only disable the apache-user script and leave your apache-sys alone, but I just didn't use it that often so I prefer to start it when I need it. I hope that helps, if you come across specific problems I can sure try and help if I came across the same.