I've just started Broken Age, and am in the middle of finding the knife in act 1. When I was looking for useful things in my inventory, I clicked on the picture of a boy, and this took me to a whole other story, which I now know is act 2.
Now, am I supposed to play acts 1 and 2 simultaneously in order to understand the story (apparently, there are links between the two acts, which are to be revealed later), or am I supposed to play one act first?
You seem to be a bit confused here. The boy and girl are two separate (but linked) stories. They can be played one after the other, or at the same time. Both stories make up Act I. Act II is not yet released, and will (probably) continue the stories of both the boy and the girl.
There is nothing that you have to do with one character that will 'block' the progress of the other, so you can play them in any way you like.
If their website is to be believed, Act II has not yet been released.
You can switch between the two playable characters/stories freely without having to fear not to understand everything, both of these stories (Shay's and Vella's) belong to Act I.
See also this question: Does the order in which you finish Broken Age (Act I) affects the ending?
The game is designed such that you can play the stories simultaneously or back to back. There are a few links between the stories, but it doesn't matter (gameplay wise) what order these links are revealed.
