You're going to have problems if you move sidecars around. I would not recommend it.
There are a bunch of good technical reasons for keeping sidecars next to the file. It avoids troubles with collisions, handles user deletes nicely, and meshes with existing standards used by subtitles, etc.
If the sidecars bother you, you could browse with Media Center so you don't see them. Or use Directory Opus, Total Commander, or other Explorer replacement that allows filtering files you don't want to see.