Hello.
The ultra-paranoid would comment that it is better to have dedicated machines / VM's for each instance, and that machine should do nothing more than be a relay. However sometimes that isn't an option so instead there is tor-instance-create.
It sounds like your problems are in a file at /usr/share/tor/tor-service-defaults-torrc. Even if in your /etc/tor/torrc file you dont enable the SOCKSport, control port etc, they will be enabled because of this service defaults file. I believe there will also be copies of this service-defaults in /use/share/tor for instances to use.
In the default configuration, tor-instance-create will end up with two relays trying to use SOCKSport 9050, enable control port at 9051 with cookie and a few other things (yet more race conditions) AND no logs so you have no idea what is happening.
Firstly, delete what you dont want from /usr/share/tor/tor-service-defaults-torrc file and its copies. Try to use /etc/tor/torr and /etc/tor/instances/instance_name/torrc for all options and it will be easier to manage.
Secondly, enable logs for all relays. You will have to change the default file from /var/log/tor/notices.log to notices_instance1.log or something for each instance. This will stop race conditions for the logs, you will have to follow the same logic for everything else (eg race to use port 9050)
Lastly, if you want to stop the "first/main" instance from running I use sudo service tor stop, but this will change depending on your machine / OS.
BTW if you delete /etc/tor/torrc apt-get will ask you displaying a screen that says "the package maintainer has shipped a new configuration file what you do want to do" with about 4/5 options. It will only (re-)install /etc/tor/torrc if you tell it to (the default option is no I think).
I hope that helps.
Thanks.