Multi site setup - root domain query


I am setting up a new multi site network but won't have access to the networks main domain until the first site is built as the new network is replacing an existing website (not on wordpress).

I know that the multi site has to be built in the root folder, but I need to know if I can use a different domain name to build the sites and then allocate the correct domain name after? How would I do this, the subdirectories will be etc and I need the correct domain to be showing on all sites in the network, but can only transfer the domain after the first site is built without creating downtime.