If you happen to read the Sins manual, their capital ships are very heavily loaded - the title of the most heavily populated ship in Sins belongs to the Jarrasul Evacuator, housing 15000 Vasari. The other four capitals have fewer crammed in, but are often over 10000 onboard.
Judging from the huge numbers of Vasari onboard their capital ships, they're probably using them as vessels to move large portions of their remaining populace, and probably shuffle personnel around to establish colonies, crew ships and structures, etc.
