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This phase introduces a new, optional system that allows your guild to mark other guilds as allies or adversaries. When the game launches, these designations will influence which guilds are placed on the same server.
*We will make reasonable efforts to place as many qualifying groups of allies and adversaries as possible together on the same server. Given the volume of anticipated guilds (as well as other factors), we unfortunately cannot guarantee that all specified allies and adversaries will be placed on your server.
It sounds like officially marking each other as adversaries would increase our chances of being placed on the same PvP server. Then we could officially interact, fight, etc. It looks like you can't use this feature yet. Here's another paragraph from the same page:
Originally posted by SWTOR Guilds FAQ
When will Phase 2: Alignment begin?
A date has not yet been determined for the beginning of Phase 2, but this phase will occur before launch. The website will be updated with information for guild members and leaders about the new features available during this phase.