Right now you need to use #clearsites as many times as the nation has default start sites, then use #startsite <site nbr> to assign new ones, up to four times.
After the next patch, using #clearsites once should do the trick.
Ok this is a three parter. Where can I find a list of the sites? What if I wanted to make a new site, how do I go about doing that? And how would it work if I wanted to add a site to a mod i've downloaded?