The best method would be to copy them to the system directory of the target machine, you will need to differentiate between OS's though since you need to use System32 on some and System on others.
I know 2000 uses System32 and Win95 uses System. I generally use Installshield and make it figure that out for me.

As far as previous version deletion.
There should be no problem deleting the older version.
The controls are found via their registry entries and that is what is used for the location. That way they can be found easily even if someone puts them in the wrong directory(as long as they register it there)