SPAM and SNOTE both update ABAP Code and Data Dictionary objects within the Database.
The SAP update manager supports more complex changes to the system. This includes Support Package Stacks and Enhancement packages, as well as Upgrades. In the case that a new kernel is required (eg. Upgrade, SP-STACK) then the new kernel will be deployed to the relevant OS filesystem.
A high level description of SUM is available at SUM for ABAP - Troubleshooting Guide - Software Logistics - SCN Wiki .
You can reference SAP note 19466 ( http://service.sap.com/sap/support/notes/19466 ) which describes the kernel patch process. This includes the location on the file system that the kernel is stored.