You know, I really can't say not having seen it. If they have a color sample either online or in paper form that would help. I would mix it custom myself, ordering both reds and finding the right balance. Also you can mix it so your first "coat" has more pigment vs. water so when you sand it down, you've really saturated the flames with color. This would be a compromise between using a darker color first. Woodworker's supply (woodworker.com) has the same dyes for the same price, but they also have a "ruby red" in addition to a crimson and a scarlet. I have the crimson, and it's alright, but I usually add a little purple to it for that rich, black cherry color. But you might find the ruby red to be just perfect. Also don't finish the guitar until at least a week after your last stain coat. It's not that it isn't "dry", it's just that water based dyes seem to bleed deeper into the wood over time, so you think you have the color just right, and it will lighten a little as the grains draw it in. Especially with a water based top coat.
As for the filler, it is usually clear or wood-tone tinted, in various shades. You can stain the mahogany, then scrape the filler on, then sand it back. If you sand through any of the stain you can re-wipe it on after the filler is cut back. You could also apply a washcoat before the filler to lock in the stain. It's just an idea. But make sure it's thin enough that it doesn't fill the pores. ESP did this on many of the Ash strats. (purple, blue, red) from the mid-90's. I think Schecter did it too.
For a first timer a clear filler might be best. You can put some of the red tint in it if you want, but if it's really clear, and not milky/chalky looking you won't need to.