Re: Question about service upgrade
JF,
Robert is exactly right in his response. You will need a 200 amp main breaker in front of the transfer switch. If I understand your installation correctly you will need a 200 amp SEU cable (3-wire) riser from the meter pan to the service drop (unless you're using PVC), then nipple into right or left for the 200 amp main disconnect, out of the disconnect with SER cable(4-wire) to the transfer switch common terminals and out of the top with SER cable to the 200 amp main lug panel. Remember the neutrals and EGS have to be separated (i.e. don't put the green ground bonding screw theough the neutral buss bar and install a separate ground buss into the backbox for the EGC's).
Check with the generator manufacturer and ask whether they recommend grounding the neutral. If they do then you can just bug the neutral through and use a 2 pole transfer switch. If they recommend that it floats then you'll need a 3-pole transfer switch. In either case you'll have to bond the EGC's to the transfer switch cabinet.
Finally, as Robert mentioned the main breaker is now adjacent to the meter and you'll have to run your cold water main ground and ground rod connections to it and not the main lug panel.
Hope this was helpful.