Most of the underlayment used has a weave that is water permeable, so any granular-type nutrients you might sprinkle will dissolve with rain or watering and travel down to the plants.
For most plants, the underlayment and rocks are usually placed with a little bit of wiggle room around each plant- you can safely push that back a bit if you think the plants would benefit…. I have done some of that, as hot rocks in summer can cook a plant if they are piled too close to the base or too high around the stems.
I use slow release fertilizer (Osmocote) on some flowering plants, liquid systemic (Bayer) fertilizer on others and granular acidic (Bougain) on others.
I also use Milorganite (granular) for our greenery (in between the professional, seasonal palm applications by Massey)
We eliminated our grass almost 3 years ago and except for a few small areas of ground cover, we have all rock now. Our flowering plants are thriving, our palms are deep green and all is well.
P.S. Resist putting the fertilizer right next to the stems. Think of your plant as an open umbrella- place the fertilizer around what they call 'the drip line'. That's where the feeder roots are. Oh- and more is not better. Follow the amount recommended for the best results… too frequent or too heavy an application wastes the product and can harm the beautiful plants you desire.