I used to present interactive PPT presentations very regularly and would have multiple programs also running in the background which I would move between for demonstration purposes. Unless your computer is on the older side or you already have issues running multiple programs at once then you should be ok with this method.

Of course your other option if possible is have two computers, 1 with the loop slides running, second with your main presentation and then have a switch box between them & the projector and just switch between the two monitors with a flick of the switch box. I have done this before also.