The whole week?
The guild that is to be used to be assigned to a server in WvW was to be selected in advance. For this BETA, that needed to be set after the game update on the 30th, and latest by 11:59pm Pacific (UTC-8) on December 2. If no guild was selected, you might be matchmade as an individual for the beta event (i.e. not with your guild). That might explain why 'your' guild is not together on the same WvW server, could it be that 'your' guild is not their (or even your own) selected/assigned WvW guild?
Linking a guild to an Alliance was/is not yet an option in this BETA. This BETA is more about large scale testing of the back-bone system. Creating your own alliances was mentioned as feature of the new WvW system, so I suspect, if they get the back-bone working, the option of creating an alliance will follow in a later BETA. So we should be able to create that community server feeling then, and even give us more control over with whom we play (though that requires our guild leaders to take initiative, if a guild does not join an alliance, then it will be assigned to a server in a much more generic way). And guildies are to be pro-active with selecting/indicating which guild they want to be considered as their WvW guild. From what I understood, you will still be able to represent one of your other guilds while in WvW, but that will not change the server you are assigned to for that period.