It is not difficult to reference a custom .NET DLL from within an SSIS script, but there are a couple of things that you will need to do:
- Sign your DLL
- Put it in the GAC (copy it to c:\windows\assembly)
- Put a second copy in the C:\Windows\Microsoft.NET\Framework\v2.0.xxxx folder
Once you have done all of these things, then it will show up in the list of available libraries when you attempt to add a reference to your script task. I found this out the hard way, so hopefully this will help at least one other person.
More details are available here.