As far as I know there is no way to communicate to freerouter to route other than in sets of two layers.
Lots of beginners expect an “autorouter” to be some kind of magical thing that does all the PCB layout for you. It is not. They can be a useful tool for some PCB’s, but they can never route a PCB properly if the footprint placement is not chosen carefully, and you only learn good footprint placement by manually routing PCB’s to get some hands-on experience. Finding the right footprint layout can be more time consuming than routing of the tracks itself.
In my experience autorouters just made a big mess of things and got a PCB “routed” for 95% in a few minutes (that was 20+ years ago, after that I just never used an autorouter) and then leave no possibility to route the last 5% and fixing it takes more time than deleting everything and routing the board manually in the first place.
Instead, my advise is to get acquainted with the interactive router in KiCad first. It has some quite nice features. For example it can push tracks and via’s aside to make room to squeeze another track in between.
The auto router usually also does not know anything about concepts such as GND planes, differential pairs and length matching.
I have also found a few mistakes in the schematic while manually routing a PCB. Looking at your work from this different perspective does help to find some mistakes. I also find manual PCB quite a fun puzzle to do. Much better than laying boring pieces of colored cardboard on a table.