You can specify a cert per-virtualhost... (makes use of server indications which is supported by nearly every modern browser). As far as making a script to install the cert automagically... This would largely be distro-specific (unless you do a lot of extra coding to make it happen) most RHEL platforms (if not all) put stuff in /etc/httpd/... where debian-flavored put it in /etc/apache2/... and who knows where else it can end up on other distros.
If you're sticking with one specific distro... keep in mind that there's also a lot of different ways to do your configs. you can have 1 singular megalithic config file that contains everything... and you can break it out into smaller components that load other configs... (i.e. how httpd.conf loads conf.d/*.conf)... or even break it up with individual configs per-site, per-module, and a dozen other ways...
By default, however, most platforms still running apache 1... traditionally have 1 megalithic config that configures all of apache... and I don't think there is an option to load additional config files. Apache 2.0.41 introduced the include with wildcards to allow things like:
which encouraged a lot more of the broken-up configs.
As a good idea, I would highly suggest you standardize your environments as much as possible. Trying to support multiple environments with multiple types of configs and multiple versions of everything is an absolute nightmare. Additionally, Apache 1 is beyond EoL. Sure, hotfixes might still be released... but I wouldn't rely on it for any kind of secure environment. I have yet to find anything that is only available in Apache 1. Apache 2 as been stable for 8 years now... it's time to upgrade.