Best Save Manager Mod/Program?

[AegisRunestone]

So, currently, I'm using Save Manager GPI to manage all my characters, but it also shows the folders for SKSE and any Facial saves I have from the ECE (see attachment).

 

I have a couple questions:

1) Is there a better save manager, and what exact steps must I take to transfer my characters over so they are safe, and work with the new save manager?

3) OR is there a way to make the current save manager I use exclude the SKSE/CME folders or be able to place my character saves in a different folder without Skyrim complaining?

 

Thanks. :)