I'm not sure that's the optimum thing you want to do and I'm not sure what you mean by primary and secondary grounds.
There are meter boxes with two 100 amp breakers that will accept a 200 amp service. There is even one that will accept a 400 amp servive and give you two 200 amp services. See
Midwest Electric Products, Inc..
That makes for a nice clean installation and the best place for the ground rod would be the meter box.
If your using two 100 amp panels, then you have to connect the ground rod at the meter and your 100 Amp panels will have to wired like sub-panels with isolated grounds and neutrals. It is permissible to use a breaker rated the same or higher than the main to use as an alternate interior disconnect, if desired.
You will need an approved method of connecting two separate circuits to the main panels at the meter.
There is a limitation on the distance between the meter and the main pannels have to be without having a disconnect outside. Furthermore, the AHJ may require an outside disconnect.
When using two ground rods be aware that there is a separation distance required. The scicky in this forum has a way to read the NEC code. You can't search, nor print, but you can read.
A reminder that it is suggested that other utilities such as phone and cable terminate at the same place the ground rod is located. Generally it's not a requiremet.
I know it didn't directly answer your question.