1st of all, make sure that your hostname is set to srv1.domain.com , use this command in putty:
hostname srv1.domain.com
Make sure that the hostname is set in your dns too (especially if you use external dns server) and the PTR is correctly set for your hostname.
Wait for a few minutes so the DNS will propagate.
After that, set the hostname in cwp admin. When you set this, the cwp will automatically generate a SSL for your hostname, and your SSL will be generated for srv1.domain.com.
The next step is to generate a SSL for your other account you created : domain.com. Enter in your CWP user panel, and generate the SSL for domain.com.
You may encounter an httpd error after this. If your httpd is doing this, in putty write:
killall -9 httpd
This code will close all the httpd unclosed connections.
Next step is to go to Dashboard, and start httpd server.