Have you got a link to your sensor?
If I've read this correctly, you're suggesting connecting the +ve and -ve to 2 separate analogue reading pins, this is not technically correct, no. The -ve would connect to gnd on a Due. I don't know the specifics of your sensor, but I suspect it will require amplification to give you a reading (P-N thermopile doesn't mean much to me or google, hence the request for a link).