If you’ve created the 3 column template. Then you just need to include the sidebars in you template only at the required place and remove elsewhere.
And assign the teplate to the required page from admin panel.
And your sidebar will be shown only when the 3 column template assigned page is rendering.
That does not seem to be the case. I only have the 2 sidebars registered in my functions.php file. That’s when they show up in Widgets. I’ve got a lot of empty sidebar containers showing up in widgets and would like to hide them when they’re not being used. I haven’t created any page templates for these sidebars.