You can add a logo overlay on output, in real time.
To add a logo, make sure your graphics card is selected in the engineering menu of the VTR Output module. If AJA_OEM2K is selected, you cannot use the Logo Overlay feature.
To select the card in the Output Clip menu:

If you do not see GFX SDI as an available option in the Graphics Card box, it is either not installed, or it is not set up or configured properly.