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I see three possibilities.

You allow users to install software on their instances manually. This requires instances to have connectivity to software repositories.

You use cloud-config to automatically install software when instances are started. cloud-config accepts YAML files that describe the things you want to do with the instance, such as installing and configuring software packages, but also adding users, uploading certificates and the like. Here again, the instance needs connectivity to software repos.

You could create images that contain the software. This way, no software repos are required.