Have you tried modeling your pebble bed as a "custom" porous media?
Is the question how to create the pattern? Or how to handle it in flow?
In flow the best way is with porous medium
Check out this article on the basics http://www.hawkridgesys.com/blog/flow-simulation-2013-parametric-studies/
The challenge will be the heat transfer properties. But the same process should be possible.
And consider some symmetry.
For modeling the balls, if they fall in uniformly, there is probably a combination of patterns that would work. Non uniformly is difficult, motion contact could help but you'll run into issues described in my presentation at sww2014 http://www.hawkridgesys.com/blog/solidworks-simulation-tools-sww2014/