Well i whould recommend Starting off with the boxes. to adjust light just put a card board box inside with a bunch of box stacked up. that way when they babies grow you take a book a way to make up for the growth. Then in later growth Make another box with Bigger lights. WARM lights all WARM lights. that can be your Flowering box. that way when your babes are ready to hit 12/12 you can germ some more seeds and transfer your babies into the 12/12 and put the germed seeds in teh veg box for veging. that way you get a system goin and have a supply of herbs every month every other month. start off with 3 or more plants and only pick the best 2 for you grow cuz they will out grow the box if you have 3 or 4 unless you planing on soging which im not sure has been done so i odnt' know about that i'd recommend LST, Scrog or both.

For intake out take
well you can do it 2 ways.

1) put on fan blowing air out on the top box on One side and on the Other side on the Bottom box, put a a hole of equal size. or a fan blowing in if the heat becomes and issue.
OR
2)put a fan on TOP of the Top box right in the middle and on the bottom box put 2 holes, One on each size of Half or Three Quarter Size.
which is the case of what im doin