Is your clear filler also a product by Golden?
Everyone has their own tricks and there’s hardly ever one “best” method, but I’ll throw mine out there too. I mask the acrylic and defocus the engraving to get it a bit smoother and I then use a quality spray paint for the coloring. I’ve tried the two-toned layered acrylic and it can be hit or miss for me . A lot of it deposits color back onto the engraved area and takes too much work to clean up for my taste.
I use a couple of different fillers, depending on what I need.
I’m certainly not trying to push the Golden brand here. (I don’t want to come off sounding like a salesman.) Golden sells lots of different kinds of clear fillers. Many of them just differ by the amount of water content. But for clear filler, there are lots of other brand options. (In my opinion, Golden is a good brand, but not always the most inexpensive.)
This is where you’re going to need to play around and experiment a little based on your needs. Some fillers sink in when they dry. (But even when they sink in, it’s a smooth slope.) After they dry, some kinds remain water solvable, some are water resistant, and some are water proof. (By “waterproof”, I mean I do the dishwasher test and they had no visible change after 5 washes.)
The nice thing about GF engraving on acrylic is that it leaves a rough “frosted” surface that most acrylic paints strongly adhere to. (No extra sanding needed.) You only need to worry about it coming off if you’re painting on the smooth surface. (And in that case, it makes for a great acrylic peel.)
Flooding the area with paint seems to have produced a better look. I also tried a luster paint that I used to use with resin and I am happy with the results!