Ok, this may sound stupid, I have been reading about separating the ground and the neutral wire once it is in the service panel, does this mean I connect another grounding bar directly to the casing of the panel along with the bond wire from the grounding rods, water line and grounds from all the branch circuits? And all the neutrals need to go on the other bars that are connected together across the panel?

No, in the main panel they are bonded. They are separated once the circuits/feeders leave the panel.
This means installing the bonding screw in a new panel and having the grounds and neutrals sharing the same bar(s).

OK, what if it is a four wire feed from the disconnect at the meter to the service panel?

ok, what if it is a four wire feed from the disconnect at the meter to the service panel?
Well, the service panel would have the main breaker in it.
Feeding form a main disconnect to a branch circuit panel is different. Then they do remain separate and isolated.

Also, the ground rod wires and bonding wires must go to the service equipment, not the branch circuit panel.

Thanks for the help