My service provider does not support Let's encrypt directly but said
"If you wish to Install third party SSL, It is advisable to upload SSL certificate bundles such as Certificate, Private key and CA bundle for your domain in cPanel under File Manager and let us know the path so that we can proceed with SSL installation."
I know how to access and add files to my site but I am not aware of exactly what they want me to upload nor how to obtain it from here.
I don't understand that part.. Do you have access to mysite.com or only to mysite.com/v5/ ?
Also, to answer your initial question:
They don't want you to upload your site the same way you upload HTML, JPG or PNG files to your website. Usually the hosting providers configuration panel (such as cPanel) offers a specific SSL part of the panel to upload said files.
It seems that rather than certifying a subdomain (v5.mysite.com), which Let's Encrypt allows, @stillblue is trying to certify a specific URL (http://mysite.com/v5), which Let's Encrypt doesn't currently allow.
It also seems that the hosting provider expects to find the certificate, CA bundle, and private key files on the hosted instance somewhere so that the hosting provider can install the certificate. This would be fine as the certificate and CA bundle would both be located in /CertSage/certificate.crt and the private key would be located in /CertSage/certificate.key if @stillblue were certifying v5.mysite.com.
RFC 5280 allows the SAN extension to contain a lot of things currently not allowed according to the CA/Browser Forum baseline requirements. Never say never, but I don't think those other SAN options will be allowed in the (far) future. So I'm enclined to say CAs will not allow specific URLs in their certificates any time soon.