I've got a code working for placing 100 (or the number you specify) circles inside the bigger circle.  Here's an example image of the placement.  I think it looks pretty realistic.  It places 100 inside at random and then adjusts each at random until none overlap by calculating the amount of overlap each time and only moving if the overlap decreases.  It's not in your matlab-to-modflow code yet, but it's a step in that direction.

Example generated image of 100 marbles in a layer

Movie done in NetLogo showing a very similar algorithm to the one we used in MATLAB.  Red marbles are overlapping and blue ones are not.