You only need a single domain certificate if it will be referenced as you described.
Depending upon your app you can have a listener to determine how you wish to call it. If it is a simple page reference it would be https://www.yourdomain.com/folder+pagename
You have to configure SSL for custom domains. Enable it in the Google App Engine billing for SNI + VIP. After this enabled use openssl to create your CSR. [I used Ubuntu linux openssl]
Make sure it is upto date and not an old version so you are not subject to the heartbleed vulnerability.
openssl req -new -newkey rsa:2048 -nodes -out www_yourdowmain_com.csr \ -keyout www_yourdowmianprivatekey_com.key -subj "/C=US/ST=Full State not the two \ letter abbreviation /L=City /O=Company Name LLC /OU=Division of company \ Information Technology /CN=www.yourdomain.com"
You will add your alternate domains at the time of purchase.
www.yourdomain.com yourdomain.com
Update your DNS records - Add CNAME record for GAE
When you get your certificate issued you have another half dozen steps depending upon the SSL issuer. The general steps to install and activate the SSL on GAE you have to upload two files: combined.pem file and you unencrypted private key. Once the files are uploaded you then select the serving role and CNAME record.
Your certificate + intermediate certificate = combined.pem file [In some cases it maybe three certificates to make the combined pem file]
private key file from CSR request
openssl rsa -in www_yourdowmianprivatekey_com.key -out unencryptedkey.pem
The Google documentation leaves a lot to be desired. If this is a domain that you plan to have for a while I would get a two year certificate. I just went through this process in the last two weeks. I have used Digicert and GoDaddy in the past. Other vendors are Verisign/Symantec, Comodo. If this is a public project you want a SSL provider that is distributed as part of the major browsers. This puts Digicert, Verisign, Comodo on the top of the list due to the length of time they have been in the marketplace. Some other providers may not be as widely accepted.