Welcome to RapidWeaver, and the forum
Themes control the appearance and layout, navigation options and (placing of) elements on your pages.
Stacks add functionality - mostly regardless of presentation, to simplify. So they really should be considered as independent of Themes.
The Stacks add-on is required for stacks; but not for Themes. The Stacks add-on (and the stacks which use it) works directly with (most modern themes for) RW. You use stacks within Stacks.
Let’s try a quick fix with one question first:
In which directory are your RW addons? There are recommendations.
You should ideally install the very latest version of Stacks.rapidweaverplugin at the root level of that ‘best’ directory. After that, next to no work at the filesystem level is required. Indeed, it may be undesirable.
It’s OK to create a subdirectory of that ‘best’ directory; I call mine Stacks - just in case. And then important to put all Stacks which you buy in that same place.
What happens when you restart both computer and RW after making sure you’re set up this way? And perform updates from within Stacks itself?
Sometimes a stack will install, needs and uses components which you do not, and which you do not need to see or use. They are ‘helpers’ if you like… some stacks are made up of several parts. You can control what you see in the Stacks library.