there are 2 ways:
1. you create containers for each group then use wayfinder to specify the start id for each group
[[Wayfinder? &startId=`1`]] - main menu
[[Wayfinder? &startId=`2`]] - right menu
[[Wayfinder? &startId=`3`]] - left menu
2. you make 3 wayfinder calls each one with the list of links you want to display
[[Wayfinder? &startId=`0` &includeDocs=`1,2,3,4,5,6`]] - main menu
[[Wayfinder? &startId=`0` &includeDocs=`7,8,9`]] - right menu
[[Wayfinder? &startId=`0` &includeDocs=`10,11,12`]] - left menu
more on parameters here
http://www.muddydogpaws.com/development/wayfinder/parameters.html
I would use first method because when you add a document to a container the link will automatically appear in the menu.
For the second method you need to add the docId to the wayfinder call