You can set a couple of package upgrade options in the designer through the SSIS options page (Tools -> Options...)
These defaults will be used anytime you upgrade a 2005 package through the designer.
See my post about the Upgrade Wizard for more details on these options.
You'll also a couple of other things on this page:
PingBack from http://msdnrss.thecoderblogs.com/2008/03/22/setting-package-upgrade-options-in-the-designer-2/
We tried to make our package upgrade as seamless as possible, but one problem we've seen people running