organize pictures into destination folders automatically based on date
You can use Hazel (http://www.noodlesoft.com/hazel.php) to organise and file your photos.

In Hazel you can create rules to act on files, these rules can be based on for example file metadata or EXIF information.
The rule actions can create new folders and subfolders from these attributes and copy the files into the right location (it can also handle file name conflicts).

I found an example to set this one up on dpreview. (In step 4.c you specify that it should only work with pictures, it will ignore the videos). 

The only thing you might need to do is to copy the files from the current folders into the folder where the Hazel rule will trigger.