It will all be fine! This is the hardest part of all! They finally start trusting you and look what you do!!! You take them away from their safe place and their momma!!! I know that is how you feel, BUT if they were still outside momma would be going away for longer and longer periods of time until she just didn't come back anymore. All kitties, and especially the wild ones are afraid of anything new. Since they know you it won't take them that long to settle down and find great adventures in their new space!!
What is your plan with Macy? Are you bringing her in for awhile to? I know you are going to get her spayed but what about after that?