How to let users set wild card domains and root domains in my single server dynamically

Aaah I see. One way you could go is to have domains being directed your way based on an A record, and have your server respond based on, as you might guess, host headers. As long as there is a single web-server responding to the incoming HTTP requests, you are free to handle it however you want to handle it.

TCP traffic is being differentiated by the destination port, destination IP, source port and source IP. The HTTP protocol is transported over TCP, and HTTP adds additional information in the host header so that multiple domains can be ran on a single server. Hence, if you have a web server running on port 80 on a certain IP address, you can run any website on it using a single server, if you only check the host header. If you wish to support SSL you have to do a bit more work, because that is literally a wrapper around the TCP protocol. Personally I would offload this responsibility to a reverse proxy, but there are reasons this might not be viable, or secure.

How I would handle that from a technical point is to set certain properties like logo and so on based on the host header, but have the rest of my application (routes) work as usual. This would be a pretty maintenance free way to allow customers use their own domains. Accepted hostnames and their properties could be configured with a database. In this case it would be beneficial to cache the values to allow quick request responses.

Allowing customers to use CNAME records for their configuration requires a bit more set-up. Given a CNAME is a redirect, which looks up the IP address of a different domain name, you would require something with which you can dynamically create DNS records. See https://github.com/AnalogJ/lexicon for example. The benefit of this approach is that when you change servers, you can update the IP configuration for your customers.