Question: After installing MySQL Community Server 5.59 (64bit) and MySQL Workbench 5.2.31a and setting it up I try accessing the db's configuration and receive the following error:

> 
> Configuration file 'C:\Program Files\MySQL\MySQL Server 5.0\my.ini' can not be found. New file will be created on apply of changes.
> 
> 
> 

I click OK. Then when trying to apply any change I get a second IO Error for not being able to write to the file.

It figures as my installation is at `C:\Program Files\MySQL\MySQL Server 5.5` and not at `C:\Program Files\MySQL\MySQL Server 5.0`. But why does Workbench search there?

Answer: 
You need to create a New Server Instance in server administration section of Workbench. There you will be able to specify your .ini file location.
Your Server instance is registered wrong.

When you create new server instance for server administration in workbench, there is a selected option, e.g.:

> 
> Mysql Installation Type:
>  Window(MySQL5.0 x64 Installer Package)
> 
> 
> 

If you selected a wrong one with your current OS and Server installation, it would result an incorrect base path mapping.

To solve your issue, you can change the base directory in Server Administration-> Logging the instance -> Configuration Menu -> Configuration -> General:
1) Click the base directory checkbox
2) Input the path e.g. 

> 
> "C:/Program Files/MySQL/MySQL Server
>  5.1/"
> 
> 
> 

3) Click the data directory checkbox
4) Input the path e.g. 

> 
> "C:/Documents and Settings/All
>  Users/Application Data/MySQL/MySQL
>  Server 5.1/Data/"
> 
> 
>