Yeah, there are a couple of ways to do that.
The mugen.cfg file controls what screenpack you are currently using.
So mugen.cfg would look like this:
motif = data/screenpack1/system.def
;motif = data/screenpack2/system.def
The one without the semi-colon is the one mugen will use. To switch, just switch the semicolon.
;motif = data/screenpack1/system.def
motif = data/screenpack2/system.def
Doing it this way is good if you have many screenpacks you want to switch often.
The other way is using a batch file.
echo =========== Screenpack 1 ===============
winmugen -r Screenpack1
"winmugen" should be whatever you have your mugen.exe called (like winmugenplus.exe would just be winmugenplus here), and the "Screenpack1" is changed to whatever you named the folder you have your screenpack in.
Put that in a text file and save as like screenpack1.bat
Put that in the same folder as your mugen.exe.
When you click the .bat file it will automatically apply the screenpack.
Doing it with the .bat file means you can make a shortcut to each screenpack on your desktop if you wanted by making a shortcut to the .bat file.