I use 6 different tracks on my Rio. I set it to loop each sound. I have one track that I combined different sounds that is 10 minutes long. All the others are from 1 to 3 minutes and all have 1 minute of silence at the end. It's simple, was cheap to build and works in every situation I've encountered.
Working with 50-100 sound tracks must be difficult. The last thing I want to have on my stand is something difficult. For that reason I've chosen the setup I have. I'd be very interested to know how well your system works and how you catalog your sounds.
Ed