Depending on how the project manager configured the transmittal package in ProjectWise, the documents in the package may be arranged into logical folders for your benefit.
If any documents in the package have references, all of the references will be included in a folder called References. Each individual reference will be in its own dmsXXX folder under the References folder to ensure that they resolve correctly when the master document is opened, after downloading and extracting the package. You can leave such references where they are. (Knowledge of the dmsXXX numbering convention is not required; these folders are created automatically when the master documents are added to the package).