I import my files from the sd card using RapidPhotoDownloader which renames the files and puts them into folders according to my templates. I don’t rename or move the raw files after this. Since the sidecar is associated with the raw filename I’ve had no issues.
When I need multiple versions say colour and bw of the same image. I make a subfolder BWpp3 and copy all the pp3’s into it before proceeding to do my colour edits. When I want to revert/tweak the bw versions again i make a colourpp3 subfolder copy the pp3 into it and then load the profile for the relevant image from the BW subfolder. It’s robust but not sophisticated way of managing multiple edits of the same file.
Output files (mainly jpegs) I move around and rename when needed. Since the exif data is still there and my files are organised in YEAR/MONTH-DAY/ folder I can always find the master raw file when I need to.
So I’ve not had any issues with sidecar files. If you rely on tagging and adding metadata in a third party software you need to be aware that Rawtherapee is not great at handling metadata.