How to organise overflowing config files and folders in the home directory and beyond!
These tools expect their .foorc file to reside in ~ so there is no easy way to "organize" this better (besides not using the -a of ls so you don't always see them :-)) unless you want to compile everything from a (appropriately) modified source yourself.

Some tools use an environment variable to read their configuration from a custom location. This is tool-specific though, you need to consult the man page to see whether this is an option.

Some people use git or similar tools to easily share configurations between systems (and also as a way to have access to old versions), see (among a ton of other sources) these links.

PS: This is a rather broad answer to a broad question. If you want specific advice for a specific tool, please ask a new question including the relevant details