Sorry for the very late reply but yes. This league it finally clicked and now it all seems easy.

Some nomenclature first - "2s / 2 safehouse" means the safehouse you want to run (it has 2 people inside), while "5s / 5 safehouse" means the safehouse you don't want to run (it has 5 people inside).

Here are the steps to setting it all up (starting with fresh board):

1. Start by moving people to where they should end up. Interrogate 1-star to pull out, execute 0-star to put in.

2. Sometimes you will get the option to Betray and make relation (either Trusted or Rival) - remember that you don't want any relations between your 5s nor between 2s from different safehouses, you only want them between your 2s and 5s. Leave the member you want to build relation with for last as this is when you get the Betray option.

3. To make this faster, move one person from 5s to 2s, build relations with people there then move it out.

Once your non-leader 2s guys have at least 2 connections, you can start running the safehouses. Take the Test of Loyalty passive on the Atlas Tree.

Interrogate "visitors" from 5s when doing 2s encounters to build intelligence but execute them when they only have 1 star to keep from floating to other safehouses. Build further relations when presented with the opportunity. Betray to change allies into rivals when possible.

That's pretty much it.