Never enough questions!
Although it seems likely that we'd need to make a topic stating which players will fight in a round when less than 5 members fight by means of a ranked list, there is nothing of the sort included in the current rules. It would be possible that wms simple took the players at random, but if the team has an inactive then (s)he is preferably put at the bottom of said list. Vault also contains the means to insert players' names, but since seedings are done before, having a ranked list in advance seems like the most logical course of action. Teams can re-arrange it when they deem fit and wms take the top x names from the list at the start of each round.
Other means of communicating which members are to participate like pms are also possible, of course, in which case having this included in the rules for all to know and see might be good. Cause I currently have no clue what would happen if a team were to have less than 5 matches.