How to have seperate .minecraft directories?

To set separate directories for Minecraft on the latest launcher, you can go to the Installations tab in the launcher, double-click the one with the hacked client, and change the game directory entry to whatever you want. To do this with a graphical file manager, you can use the browse button to bring up Finder, File Explorer, or Nautilus so you can manually select the appropriate folder.

Sigma Client does not support custom loader directories. Its staff have stated before the only way to play with it (other than some convoluted techniques that I could find on Reddit) is using the official Minecraft launcher. It is not compatible with MultiMC or other multi-instance launchers. However, you will not be banned if you have a hacked client in your .minecraft directory, as long as it isn't the selected profile, there is no way for it to be detected.