You have 2 different issues. First is how to get stuff from the MBP to the MBA. The setup/migration assistant copy data, they don't move it from one computer to the other. So you may safely use the setup assistant when you get the computer or use the migration assistant afterwards to move your stuff to the new computer.
The second issue is keeping the two computers in sync - when I first began using both a desktop and a notebook this was a maior headache. If you are willing to use the cloud it is now easy. If you don't already have an iCloud account, get one. It is free and the easy way to keep your contacts, calendar, notes, and lots of other data synced. However it probably isn't going to be your only solution because not all software is cloud compliant - Microsoft I'm talking to you.
I use DropBox to sync my two computers - the only data I have that's too sensitive to put into the cloud is data that only needs to be on my deskop computer anyway. There are several products similar to DropBox but I find DB to be the simplest and most reliable - I've tested several.
You can also use 'sneaker net' - use a thumb drive to transfer data from one to another - what a pain. I always found that I either didn't remember to put it on my thumb drive or when I thought of it I didn't have it handy. At one time I use folder syncing software to keep my data in sync but it was cumbersome and I often remembered that I needed to sync when I wasn't near my desktop.