So basically the Groups are for reporting and have nothing to do with Node organization, right? If I understand this correctly, you can setup custom dynamic queries in the Groups so you can report on the information you seek, this is the Group features purpose.
This is one HUGE managing component that is missing from SAM. This is how it should work:
Create Group > Assign Application templates require by group > Import Nodes and assign to Group > Nodes automatically get the monitors in those templates. This would make life simple.