Hi,
Commerce configuration is configured at the site level so all stores within a site will use the same PayPal account. In the case of multiple sites its possible to configure each site with the same PayPal account, but since PayPal only gives you one setting for the PDT/IPN urls, I'm not sure it can work, we do pass the pdt url in the request I think so maybe it can but I have not tried that scenario.
Hope it helps,
Joe