I have multiple Virtual Machines with each an nginx server hosting multiple websites each.
I have some clients using historically let's encrypt and our organization can also now use SECTIGO.
How do i implement SECTIGO and Let's encrypt on the same server? Is it possible?
Can i organize multiple directories?
Yep, the answer is yes -- Caddy actually does this by default. (Let's Encrypt and ZeroSSL, a Sectigo reseller.) If one CA is down, it will try the other one.
You mention multiple VMs but do not mention if they are all behind a single IP or individual IPs.
You mention nginx but don't mention the O/Ses involved.
If you break that single question into two questions (and provide the answers), you may get us closer to answering your question.
How would you like to implement SECTIGO on that server?
How would you like to implement Let's Encrypt on that server?