In this post, you will be able to understand what the alliance network is and how it functions to help you better understand what it is.
The alliance network is basically a network in which resistance groups can join to ally with eachother. They join the same frequency and if required, help eachother out. Example, civiwatch will provide any alliance group with basic supplies if needed. Stronghold will assist Outcasts if they get in a fight with the combine. Basically, they work together when eneded, but function independantly.
The facility is the headquarters for the alliance AS WELL as the headquarters for the allied group, Civiwatch. Civiwatch does not lead the alliance network, however their leader Leonard Wong is the director of the network. Leonard may be giving control of Civiwatch to his second in command if the network grows bigger and things get too busy for him to do Civiwatch ops.
Here's a half assed diagram of the alliance network to this date:
Stronghold The Liberation Movement
\ /
\ /
Civiwatch----------ALLIED----------------------- Clinic (suspended)
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|
Outcasts
As you can see, no single group has higher authority then any other. Each group does their own chosen duties. Any group can join the alliance if they prove to be an efficient, non-hostile, functioning resistance group of three or more members.
I hope this answers your questions and gets you to stop calling the civiwatch group the alliance.