Yes, you should control
logrotate by editing files in
/etc/logrotate.conf.d. First, read
man logrotate logrotate.conf.
Some packages take special care to preserve user configuration changes, as explained in their
logrotate is not such a package.
The packaging system has been known to warn that it's about to replace a user-modified configuration file and offer choices (Replace the file, Do not replace the file, Diff the old and new files, Open a shell), but this might depend on the packager marking the file as "configuration".
A System Administration way of maintaining your modified configuration files is to store the modified files in your own, similarly structured directory structure, e.g.
$HOME/.userconfig/etc/logrotate.d/nginx.conf, and write a simple script to copy the files from
$HOME/.userconfig/ to the system. Run this script after you update the packages.
Beware! If the package changelog says "We changed/improved the configuration file format", stuff may break.