I just learned that you can only create a maximum of 3 iOS distribution certificates
in the Apple Dev Center.
I'm pretty new to iOS development, what is the common way to use the certificates?
Should I create one distribution certificate to sign all my different iOS apps with it?
Yes, it's standard practice to just use one certificate to sign all distribution binaries.
I previously worked at 2 very large, prominent software companies and they both did it this way. Each had their own custom protocols/systems in place for limiting who could create binaries using the certificate.