The way I use Freerouter in Kicad is as follows:
1 - Get the components laid out in Pcbnew and then click the yellow diamond icon with the up and down arrows on it
2 - Select 'Export a Specctra Design and Launch Freerouter', then just click save on the screen that now opens
3 - Do the auto routing and when it is done and you are happy with it select 'Export Specctra Session File' from the bottom of the file menu
4 - Click 'Save and Exit' from the file menu
5 - Freerouter now closes and you are back in Kicad, select 'Back Import the Specctra Session File' from the bottom of the list
6 - Click 'Open' on the screen that now opens and then click 'Yes' when asked to 'Rebuild Connectivity Data'
7 - All your new routing will now appear
I have been using Freerouter quite a bit recently and am extremely happy with how it works and it certainly saves lots of time if you want to get a board routed quickly for testing. I usually do a few manual tweaks just to make the routing how I like it to look but this may not really be necessary.