We have been relying to plugin commander to allow user to enable and disable plugins per blog/ site. However, having the link to your plugins show up under
Dashboard → Posts → Plugins

Is not the most intuitive. Luckily the developers have though of that and make the plug in easy to modify.
Take a look at theline 34 of the plugin-commander.php file. Which should read something like

 define('PC_PLUGINS_HOME','edit.php');

and change it to 

define('PC_PLUGINS_HOME','tools.php');

if you want the link to show up under Dashboard → Tools → Plugins
instead or change it to 

define('PC_PLUGINS_HOME','options-general.php');

if you want the link to show up under Dashboard → Settings → Plugins.

Here is some WordPress developer documentation, if you would like to know more about the whole process.

Please note that modifying a plugin to suite your need is never a great idea, because it will make updating the plugin in the future more difficult. You will have to go back and figure out what change you need to make to make it work the way you want again.