Go to Main >> SSL/TLS >> Install a SSL Certificate and Setup the Domain
Then click on the button browse and from there select the domain for which you want to install the cert for.
After that give the ip address and then press submit .
Also you should have a dedicated ip for this domain to install the cert.
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How do I install an SSL Cert with just the .key and .crt in root WHM?
Another alternative is ftp relevant domains and copy crt in certs directory after ftp, key in key directory, i suggest better use cpanel for that, so you can cross check your home work, and if you have CSR as well that is also good.