Most of Capacitor is configured per-platform; meaning that you will make most configuration changes in the native project using native tooling.
Native Project Management
Configuring a Capacitor project is no different from configuring any iOS or Android project. Existing native developers can easily work alongside web developers; with each side using the tools and SDKs they know best. While mobile application is a bit different than web development, we believe web developers can handle all the required native configuration on their own, and the Capacitor team provides documentation on things like how to deploy to the Apple App Stores or the Google Play Store to help fill in knowledge gaps.
Capacitor Configuration File
Capacitor specific configuration is handled in the Capacitor Configuration File. These generally don't modify native functionality, but control Capacitor's tooling. This config file includes things such as, setting the web directory to copy on
npx cap sync, specifying the Android or iOS project folder, or setting the App ID/Name in your native project.
iOS and Android each have configuration guides walking through making common changes to their behavior: