I have installed a 200 Amp meter upgraded from the old 60 amp and then installed a 200 disconnect with a breaker type switch inside then feeding 200 amp main panel. My question is do I bond neutral and ground together in the disconnect then run a separate ground to the panel and keep neutrals separate in that panel box and treat it like a sub panel or leave them unbonded in the disconnect and bond them in the panel?
You need a proper transfer switch in order to legally and safely use that generator
Your first order of business here is to throw away the suicide cord (after chopping it into pieces that is) and get a proper inlet box, generator cord, and most importantly, a proper transfer switch for your application, so that you don't get blamed for a fried linesman, or written up for a blatant Code violation for that matter.
In your situation, especially considering that you are going to be going generator shopping, you will also have to deal with the other point many people who put generator setups in get snagged on; namely, neutral/ground bonding. You see, most portable generators come from the factory with neutral and ground bonded together, so they can be safely and legally used for portable power applications, such as those found on jobsites. However, the service disconnect sitting on the outside of your house also has a neutral-ground bond inside it, and putting the two bonds in parallel causes current to flow places it's not supposed to go.
As a result, most residential (portable generator) transfer applications require a transfer switch/panel with a switched neutral, so that the generator's bond and the house's bond are kept separate. Fortunately, there are a few transfer panels out there that can provide a switched neutral alongside the other conveniences one comes to expect from a transfer switch. Most notable among them would be the Reliance Controls XRK models from their Panel/Link X series, as they can legally take most (GE THQL being the only exception) 1" breakers, and can be ordered through a variety of dealers (including online sellers) for a reasonable price. If your existing 200A subpanel uses 3/4" breakers (CH or QO), then you may wish to look at other options, though. Eaton makes a switching-neutral CH transfer panel (the CH10GEN50xxSN parts) that matches existing CH panels, and while Square-D doesn't make a single product that's directly suitable, they do make the requisite parts needed to field-fabricate such a transfer panel from a suitable QO loadcenter.
Once you get that transfer switch in...
Once you get a suitable transfer switch in, we can then move onto grounding and bonding considerations as part of the installation of both your subpanel and the transfer switch, which in all likelihood will be treated as a subpanel of your indoor subpanel (which is fine). In both cases, you'll be running 4 wires (hot, hot, neutral, ground) from the power source (disconnect to subpanel, subpanel to transfer switch) to the destination, and leaving the bonding means (bonding screw or bonding strap) out when you reach said destination. Furthermore, you'll also need to run a 4-wire feed from the inlet box over to the transfer switch, just like you were running a feeder to a subpanel as described above.