Ryan,
I just dusted the bottom of the grooves (1/16" deep), then poured the clear to fill. The colors always tend to settle to the bottom and I've found with mica that that settles down if I mix up a lean amount with the resin.
It really takes a lot of mica to get the colors to fully fill.
Problem I have with this cross is the black edges distract and the layer of color is uneven.
I basically dumped it in then pushed it around with a stick. I could have done better by using a sifter to sprinkle it more even. The overslop doesn't matter since that gets sanded away.

Never really had issues with the final clarity, just sand flat and final ROS sanding with 300 or maybe 400 grit.