Yes, you can assign different subdomains of the same domain to different apps in app-engine.
In the new console navigate to Compute > App Engine > Settings, switch to the Custom Domains tab and click Add a custom domain. First you must verify your domain (if not done for this app yet), then select the subdomain for the current app. Update the corresponding CNAME entries in your DNS. You have to repeat all steps for each app and sub-domain. Of course you cannot assign the same subdomain to more than one app (or using it for some other server or services, e.g. sites in Google Apps). The same applies to the naked domain. The naked domain can be assigned to only one app (or server, site).
There is also a
SSL Certificates tab, where you can add your certificates to the app and I recommend to do so. If you have a wildcard certificate for
*.mydomain.com, you can re-use it in more than one app, too. The setup for custom domains and certificates is pretty straight forward since they moved it into the new console.