as fare as I know NewCS is only a cardserver to read and access local cards and require an additional server like Mgcamd to decode channels
there should be no problem to use NewCS with a local card in addition with a cs-server subscription
as emulator you should use Mgcamd (1.35 if available for your
receiver) and its no problem to add several lines to the newcamd.list. Mgcamd will send the decoding requestes "automatically" to the local card/NewCS or the cs-server depending on the package/caid used by the channel you want to decode.
I do not know which receiver and cards you have as result of lack informations from you but if possible/available for your receiver I would suggest to use Oscam instead of NewCS. In many cases you can use Oscam in dvbapi-mode,so only one emu/cardreader-software is required and not 2 separate programms