Hi kayX, welcome...

If it is JBL soil or JBL Aquabasis Plus to be precise, the usage of this bottom layer soil (any brand of bottom layer soil/fertiliser, for that matter) as directly quoted from www.jbl.de website is :

Spread AquaBasis plus in an even layer of about 2 cm thickness at the bottom of the aquarium (contents sufficient for approx. 100 l). Place a 4 cm layer of washed gravel with a grain size of 2-3 cm on top. Do not use any larger sized gravel! When filling the tank with water use a flat plate, a panel of glass or another flat object held under the water jet to prevent the gravel from chuming up and clouding the water. The aquarium can now be stocked with plants.

As for the fertilizer balls that you mentioned, it is usually buried deep inside the gravel to prevent the kind of problem that you are facing..

Regards