I'm talking mainly about the TV series.
When the dragons were younger, she kept them in the cage most of the time (right?). Then they grew up a bit more, and they mostly stayed beside her. In the fourth season, we see that they are fairly grown (although not fully grown yet), they are not usually beside their mother, and they are more wild.
- So when did Daenerys decide not to put them in the cage anymore? (At what age and size of the dragons?)
- In the fourth season, why don't we see the dragons that much?
Related questions: For example, when Daenerys reached Meereen, where are the dragons? Are they always flying freely and to further places? Do they come back to their mother whenever they want? Can Daenerys call them when they are far away? Do they sleep beside their mother?
Note: There might be more details in the book also.