Is there a way to publish pdf or any other binary files to a specific folders on the website? Part of my site is used for document repository and I need content manager an ability to simply upload/deploy documents.
Based on your question, it looks like you want to publish binaries to a certain location. You can add configuration in the cd_storage_conf on the deployer to deploy the binaries at any given location.
Step 1: add the new storage under "Storages" assuming you have a different default storage for all other content
<Storage Type="filesystem" Class="com.tridion.storage.filesystem.FSDAOFactory" Id="defaultFile" defaultFilesystem="false">
Step 2: Configure which files you want to deploy to the above location by specifying the item type mapping under the "ItemTypes" element like:
<Item typeMapping="Binary" itemExtension=".pdf" storageId="defaultFile"/>
After this configuration, all the .pdf files will be deployed to the given location.
The location of published binaries can be specified as a structure group when calling AddBinary. This can get surprisingly complex. There are several articles on the Internet on this subject that can help you to understand what the difficulties can be. My own article on this is published on the Indivirtual Blog, and at the bottom there are links to some others.