This is a tutorial for setting up multiple instances with SAM, with screenshots of all the settings/dialog boxes, since a lot of people seem to have issues with setting this up correctly.
NOTE: This only works with SAM 4.9.4 or newer (and all SAM 2013.x) versions.
First add the /INSTANCE= parameter (after a space) on the end of the target link in the SAM shortcut (I recommend you make a second copy of the shortcut, and add this to your second shortcut), like this:

Then run SAM using that shortcut.
You should get this prompt, telling you that the activation is expired:

This is because SAM requires a second license/serial number to run a second instance.
Click the OK button.
You should get this screen:

Enter your second serial number, and select how you want SAM to activate.
Click Next.
SAM should activate, and then bring you to the setup window:

Click Next.
SAM should now show you the database selection screen:

Assuming you're using MySQL (and you should be), make sure it is selected (it should be the default), and click Next.
SAM will now take you to the database system login details page:

Assuming you're going to be using a separate database instance from your main SAM instance, click the "Specify custom settings" option.
Enter your database root password, which you should have set up when you initially installed MySQL (I believe it is blank by default, but you can check your SAMBC.core.xml file for your main SAM instance if you're not sure), and change the Database entry to whatever you want to call the new database - I used SAMDB2:

Click Next.
SAM will now take you to the Add audio files page.
I normally deselect the first option, and keep the second option selected:

Click Next.
SAM will now take you to the sound device selection page:

I normally select the "No sound device (Use Silent Output)" option, if I don't want to hear SAM's output over my speakers. This can always be changed later on in the SAM audio settings.
Click Next.
SAM will now take you (assuming you entered your database info correctly) to a screen where you'll see your serial number, but since this was already set up earlier, it won't be editable, and it will appear somewhat frozen while SAM copies the files to the data folder for the new instance that you just set up.
SAM will now take you to the Stream Hosting page, where it offers you to use SpacialNet:

Assuming you already have a hosting provider, click Next.
You should now get the Setup Completed page:

Click Finish.
SAM should now add any audio files you selected, and open the main SAM interface:

If you go to your Spacial Audio data folder (paste %LocalAppData%\SpacialAudio into an Explorer window in Windows Vista/7/8, and %USERPROFILE%\Local Settings\Application Data on Windows XP), you should now see this:

The second folder should be named whatever you set your /INSTANCE= parameter to.
This folder contains all the configuration files for the second SAM instance, including the SAMBC.core.xml file.
These files are independent of the first, original SAM instance configuration files.
And if you open MySQL Workbench (or any other tool that lets you see the database tables), you should see both tables there:

That should be it - you can now add files to your second SAM instance independently of your initial SAM instance, without the need to install anything additional.