Q: I am trying to use migration assistant to transfer my application, but my mac pro can't seem to find my mac air

How are  you connecting the two? What are you doing to transfer data? What exact models of hardware do you have and what OS X versions are they running?

At the very least you must enable File Sharing on the Mac Pro. You need to share the Mac Pro's disk via Press COMMAND-I to open the Get Info window. Check the Share option in the upper panel.

Then you will need to sign into the shared drive from the MBA.

Mac Basics- File Sharing

Mac 101- File sharing