I have a Main load center that is configured like a sub panel. By this I mean that neutral is isolated. At the SE after the Meter there is a service disconnect then an aerial drop to the Main load center. I want to run a 60amp sub panel off this panel. Is this OK? Can I be connected like a normal sub panel?

Sure, just wire it just like your main panel with the neutral bar insulated and isolated, and the equipment ground bar bolted directly to the panel's metal box.

FYI, there is no actual definition in the code for "subpanel",even thou the word is used when a panel is fed by another panel. As you noted your Main panel is wired "like" a subpanel, the issue is once the feeder leaves the box that contains the main service disconnect, the neutral and ground is separated, so it appears to a subpanel.

Not assuming you don't understand, just taking this opportunity to explain a bit more about the topic.