I have a residentail home with two meters one service drop one panel has geothermal heat and associated equipment they other has all the common household circuits my customr would like to install a standby generator and would like heat panel and a few general duty circuits from second panel question is can I have more than one autotransfer switch associated with the same generator ?

Yes you can... but the best scenario would be to add a subpanel w/ only the circuits you wish to run off generator. Unless they want to be able to run entire house from generator, then you would use a 2 transfer switch setup.