How to get plugin configuration through plugin manager?
The plugin manager is not responsible for storing the configuration, that happens somewhere else.

Typically plugin configuration is then stored in a config entity, either in a 1:1 relation (e.g. blocks) or 1:n (e.g. views, view/form displays, filter formats).

I'd suggest that you look at those modules to see how they work, block is probably one of the simpler cases in core. You can also ask more specific questions if you're stuck on implementing that