During this phase, guild leaders can establish up to three guilds as their Allies or Adversaries (depending on the target guild's faction). Not only will this help to cement friendships and rivalries, but BioWare says that these connections "will have the highest chance of being placed in the game together, allowing these guilds to coexist on the same server." This won't happen if the guilds have chosen different server rulesets, however.
Another new feature that's come with this phase is the ability for leaders and officers to begin inviting people to the guild by email. The SWTOR website has a helpful FAQ for all three phases of guild preparations. The third phase, deployment, is scheduled to occur shortly before launch and will begin placing guilds on servers if these guilds have met certain criteria.