It sounds like you used the DTS to SSIS migration tool on your packages. It has been my experience that this tool will attempt to convert your packages and any part which can't be converted will be converted into a separate DTS package and called from the new SSIS package. If your packages are showing up in the SSIS area then you probubly ran the upgrade utility.
I am in the middle of my first migration to SQL2005 right now so I am learning all this right along with you. I am hoping to import all my jobs to the legacy area and run them from their until I get time upgrade them to SSIS. I haven't yet had a successful run but hopefully I will soon.
BTW, to amend what I said above reguarding opening legacy DTS packages. That is the method which MS says should work, however I have only gotten errors so far when trying to open the legacy packages.