My understanding is that since this is a new covenant, we'll each have to set up our own labs from scratch. We can do that either before the saga starts (by slating that time in our pre-saga advancement) or in-character once the saga has started. Unless we want to describe a reason for basic labs to be already set up.
Personally, I've kept the last year of my magus' pre-saga advancement free for such things as setting up his lab, as well as gathering the last-minute resources.
The last update of the covenant's layout is in this post. As you can see, the labs are identified with numbers, so we can discuss who wants which lab.
There are 6 sancta at the main site location, and there were also plans for a secondary location a few miles away from the main site (I'm no longer sure who would use it). Other small auras also exist throughout the area. So we can always detail another area if some of the players want something special for their magus.