The last time I checked you could do this with the reseller account permissions. I do not see that being that hard. If you set up your package in whm to have two ip's and their own nameservers. Then enter it into modernbill as just a package you should be good to go.
It can auto provision IPs but its not really done on modernbills side. When you create a cpanel package, it'll contact the cpanel server, asking for a dedicated IP to be assigned to the new account. If that new server has IPs to provision, then it does so automatically.