If you can wrangle them into a single folder e.g
.zips you could keep that folder within the Library folder via this feature
I'm OCD about keeping things as close as possible to where I think they ought be. If they are inside the library folder then they will get backed up with it.
On Windows/NTFS, the only significance of the '
.' at the front of the folder names is to gather them at top of list. IIRC on Linux/Ext and/or MacOS/APFS it has greater significance.
BR