Yes, to make it run in the background create a shortcut to the batch file and go into the properties. I'm on a Linux machine ATM but I believe the option you are wanting is in the advanced tab.
You can also run your batch script through a vbs script like this:
'HideBat.vbs
CreateObject("Wscript.Shell").Run "your_batch_file.bat", 0, True
This will execute your batch file with no cmd window shown.