That's an interesting question. I think Toolbox will be OK since it doesn't look for the path on it for check in. It's looking for the hidden IsFastener property value.
For the Design Library, PDMWorks has a Standard Library tab where you define the path to that library. The problem is that the path is what the PDMWorks server sees, not the end user. So if your Design Library is now on your C:\VaultName\Design Library path, then the PDMWorks server needs to be able to see that same path. You could install the Vault View on the server, but then you might have to keep the local cache update all the time - that would be a headache.
Anyone else see a problem with this? I've never tried to manage a DL in both vaults at the same time.