I am wondering what would be a good bet to put in the two media containers in my new Emperor filter. Right now they are empty but I want to put them to use and I would like some more professional opinions on what to look at using. Thank so much!

I put ceramic cylinders in there. Lots of room for biobugs to grow!!

For smaller filters, that have limited space for bio-media, I like Eheim's Ehfisubstrat. The smaller size of the Ehfisubstrat will allow you to get more bio-media in your baskets.

I use ceramic cylinders as well in my Emperor mainly because I have a bare bottom tank setup.