how can i transfer data from my imac to my macbook air?

one of ways to do this is Migration Assistant

http://support.apple.com/kb/HT4889

I used my migration assistant with my 'time machine' external drive via USB. I have since found that all the email folders are empty. I discovered that the missing file folders were transferred, the macbook has developed a problem since. I think they are all on the time machine. I had to reformat the external hard drive after transferring the information, I thought that I can not go back to it for the missing files but now I think they are all there, I just have to find a way to get them.