If company policy requires it, you can replace some or all certificates used in vSphere with certificates that are signed by a third-party or enterprise CA. If you do that, VMCA is not in your certificate chain. You are responsible for storing all vCenter certificates in VECS.
You can replace all certificates or use a hybrid solution. For example, consider replacing all certificates that are used for network traffic but leaving VMCA-signed solution user certificates. Solution user certificates are used only for authentication to vCenter Single Sign-On.
If you do not want to use VMCA, you are responsible for replacing all certificates yourself, for provisioning new components with certificates, and for keeping track of certificate expiration.
Even if you decide to use custom certificates, you can still use the VMware Certificate Manager utility for certificate replacement. See Replace All Certificates with Custom Certificate (Certificate Manager).
If you encounter problems with vSphere Auto Deploy after replacing certificates, see the VMware knowledge base article at http://kb.vmware.com/kb/2000988.