HELP!
I need to merge the content of several large folders on my mac.
Filemanagement with Windows and Mac OS X differs, when it comes to folder replacement.
Under Windows if you have two folders with the same name, the windows explorer will warn you, that files within that folder will be replaced with the ones you just dragged in. As the result, you will have a folder containing all the files form you source-folder accompanied by the ones in your target-folder, that were not present in the source-folder.

WATCH OUT!
Under OS X, if you drag a source-folder on a folder containing an equally named target-folder, you will replace your target-folder with the source-folder. Data that was not present in the source-folder will be lost! Merging data is not trivial under OS X.
The Kingsize-Solution to leave newer Data untouched is the rsync comand. This is the way you want to choose, if you are unsure, if you updated files within both folders.

Example
We have a TEST Folder within the Source Folder, we want to merge with the TEST Folder inside DROPIN. We use the folowing comand from within the terminal.

rsync -au SOURCE/ DROPIN

-a stands for the archive option; -u leaves newer files in the destination folder untouched.

For those of you who want to save some typing and use drag an drop:

rsync -au "dragged sourcefolder icon" "dragged targetfolder icon with the last forwardslash removed"

Another option is the ditto comand, which copies the files and adds the ones that were not present before as well as overwrites the ones that were present in both folders.

ditto SOURCE DROPIN

See the internet for the many more options these comands have or use the option -h. Especially rsync has options to configure what exact files you want replaced, like timestamp, filesize or type.

Of course you should try this out for yourself, to prevent unwanted data loss!