You can use the /ConfigFile option of the dtexec.exe utility to specify a a XML configuration file at run time. NOTE THAT you cannot use the /ConfigFile option to replace configured values that you also specified at design time.
See the DTExec documentation here: http://technet.microsoft.com/en-us/library/ms162810(v=sql.105).aspx
And the SSIS package configuration documentation here: http://technet.microsoft.com/en-us/library/ms141682(v=sql.105).aspx