This is already provided for in mGalaxy, thanks to its database editor (which is one of the most powerful, all frontend included)
Click on the header on which you want to sort (with each click it changes the sorting order). So you will have all the games sorted on the presence of a logo or not
Selects the first one then clicks on the last one (with the Shift key pressed, as for any multi-selection in Windows)
Go to the DBEdit tab, click on the drop-down menu to the right of the update button and select "Selected only".
You can finally click on the update button