With all due respect to @Lialos’s comment, if you look at honey bee swarms in the wild, they will preferentially choose a new home which has about the volume of one deep Langstroth box (research done by Thomas Seeley - famous bee researcher, available free in a very readable booklet here - https://ecommons.cornell.edu/bitstream/handle/1813/2653/Bait%20Hives%20for%20Honey%20Bees.pdf). This gives them enough space for brood and honey, but not too much to warm and defend. He tried lots of different sized homes, but that was the size they chose when allowed to make their own decision. It follows that this might be the best size to start with for a new swarm.
If you use the search tool at the top right, you will see that this subject has been covered extensively in the Forum.
To summarize for you, the Flow hive should be treated in exactly the same way as any traditional hive. If you read the basic books on beekeeping (e.g. Beekeeping for Dummies) they tell you always to fill one box before adding the next. If you got a swarm 2 weeks ago, you should probably only have one box in your hive setup at the moment, unless your swarm was humongous. If you give them too much space, they can’t heat or defend it.
To decide when to add the next box, I use the following rules, that the existing box has:
- Fully drawn comb covering most of every frame, and
- The comb is 80% full of brood, pollen or honey, and
- Every frame is well covered with bees
This rule applies to adding second brood boxes and honey supers. In other words, after adding the second brood box, I would wait until those rules were satisfied before adding the super (traditional or Flow super). That makes sure that there are always enough bees to use the space, heat it, and defend it.
You mean the second deep box that you are not going to harvest? It should be plenty. 
My SoCal bees have double deeps for winter, and they do just fine.