You are doing an upgrade from 6.0.0 to 6.0 update 3f so you need to be looking at the vSphere upgrade guide for 6.0 and not 6.5. You are only doing a patch install though and not an upgrade as you are just updating to a newer minor version of vSphere as you aren't going to 6.5 or 6.7.
I would advise you to use the VMware Compatibility matrixes VMware Product Interoperability Matrices to check the version of NSX you are running is supported with vCenter 6.0 U3, and also to check the Upgrade path for 6.0 to 6.0 U3, which should be a single upgrade. Also check your hardware for the ESXi hosts is still certified for running ESXi 6.0 U3 and if there are any additional drivers/firmware updates which you may want to apply at the same time.
Once you know everything is certified and supported you will need to confirm your vCenter/PSC configuration is supported, you haven't said if you are using the appliance version of vCenter or a Windows deployment, and whether your PSC is embedded or external. Refer to the vSphere 6.0 U3 release notes VMware vCenter Server 6.0 Update 3 Release Notes for information on the recommended deployment models, and see the VMware documentation http://pubs.vmware.com/vsphere-60/topic/com.vmware.vsphere.install.doc/GUID-7C9A1E23-7FCD-4295-9CB1-... for more details.
Then you can download the software for the upgrade from the VMware website, you will want the update bundle for the type of vCenter you are using (Windows or Appliance) rather than the full bundle that is used to deploy a fresh instance of vCenter and PSC.
There is also a link in the release notes for the vSphere Upgrade Guide About vSphere Upgrade which contains flow diagrams relating to upgrading to vSphere 6, but as mentioned you are patching the vCenter so you really need to refer to Patching the vCenter Server Appliance and Platform Services Controller Appliance section of the VMware documentation instead. That will take you through the process to install the U3f patch onto the vCenter and PSC and you can then use Update Manager to update the ESXi hosts to 6.0 U3 if you want to.
As it is a patch install there is no change to the size of the appliance (or Windows server) from the original deployment.
