Odd... Add > File(s) should add a single file or files to the folder from which you issue the context menu command, regardless of the path in your working folder. Not sure what's up with that.
I think
crzyrndm is suggesting that you mirror the folder structure you want for the mod pack in your working folder (on desktop, or wherever), then use Add > Directory, instead of Add > File(s), to pack up the whole thing. That's one way that should avoid your issue and is probably good form, in general.
You could also use Add > From Pack to select and import the files (or whole directories) you want to edit from the vanilla pack (e.g. models_rome2.pack). That will keep the original path and folder structure intact. Save the pack. You can then extract the whole thing to create a working folder with correct paths. After editing, you can use either Add Directory to pack up everything or Replace File (which is in the top File menu, not the context menu

) for individual files. Add File(s) should work as expected though, at least it does for me.
One thing that is currently bugged with PFM is the ability to 'edit in place'. That's where you double click a file (or issue Open > Open External...) for editing. PFM then asks you if you want to overwrite the packed file with the edited copy. However, it only works once per PFM session as it gets stuck on the first instance of the temporary file copy. Drag and drop does work for individual files, but you have to use Replace File to get it back in.
Hope that helps.