The global configuration command - config-register is used to modify the behaviour of the router. Weather or not it boots from saved configuration. Weather or not it boots from the flash or the boot-proms.
The following page is an excellent reference for configuration registers http://www.cisco.com/univercd/cc/td/doc/product/access/acs_mod/cis4000/4000m/4000sig/vconfig.htm
In summary these Boot Registers are quite handy: