Migration Assistant is an all or nothing process. What that means is when you launch MA it asks if you want to migrate:
- Settings
- Data
- Applications
You simply check the boxes of the above items you want migrated and it will migrate all of items in the boxes you selected from either your Time Machine backup External Hard Disk OR your MBP. In your case because your MM only has 512GB of storage my recommendation is to only migrate the Settings and Apps from the MBP to the MM. Then you will have to manually copy and paste all of your data that you stored on the MBP to the External Hard Disk connected to the MM.
To be very honest, you should have purchased a MM with 2 TB of storage that way the migration would have been dead simple. If you are still within your 2 week return period for the MM that is something to seriously consider. By trying to save money by only buying a 512GB MM you are forced to buy an external HD or SSD and manually move your data files which is tedious, error prone and VERY time consuming.