I am new to Drupal/Drush. I tried to learn Drupal last year with tutorial that was based on Acquia-drupal (which I downloaded and was using drush there). Now, i decided to give it another go by installing Drupal on MAMP. I tried to download a few development modules and the operation was a succes, but the modules didn't appear in my list of modules. Than it dawned on me that they must ended up on the wrong location instead at my new MAMP/sites/all/modules... How do I fix that - do I ought to delete the Acquia, or should I install another instance of drush?
Drush is path-sensitive and can be installed system-wide; no need to install a separate instance.
To run Drush commands in the context of a site, you need to be in the web root of that site.
drush cc all; // Clears cache for the current site only
If you run commands outside of a Drupal root, the effects will vary. Modules will be downloaded to the current folder, cache-clear will clear Drush's internal cache, and some commands simply won't work as they don't make sense without a Drupal boostrap.