I wasn't clear: in case you want to change it (for instance, to configure which version of TLS is supported), you'll have to do it for each subdomain instead of one time. That's the issue with multiples subdomains.
For that you just need to redirect different subdomains to your server, and inside of Yunohost admin interface (or command line if you prefer), add all the domains. When installing your app, you can then choose the subdomain you want.
Don't forget that you can install in the root / of a domain (and have only one app) or multiples in /myapp1, /myapp2, ... As you prefer