Conor, there are basically two ways to color your finish - you can either apply stain directly to the wood which usually absorbs it at different rate depending on grain and cell structure or you can add it to your finish and tint the lacquer or whatever you are applying. I discussed this briefly in the current thread about finishing a Guitar Fetish tele, but to repeat, wiping stain directly onto the wood is a traditional way to pop the grain of highly figured wood. More stain is absorbed into the "flame", hence it will be darker or brighter or whatever you are trying to do. It is also darn hard to control - the cardinal rule of practice on scrap applies here more than almost anywhere else. The other cardinal rule is that if you screw up you are pretty much doomed. (pictures at the other thread)
The second way to pop grain without staining the wood is to use something like epoxy or CA as your base coat. If the wood needs pore filling then epoxy can be a great filler. This is some highly figured koa which was pore filled with Zpoxy (available at LMII) and then clear coated with a waterborn lacquer.
I'm currently building a guitar out of highly figured cocobolo and plan to use the same products on it.
The other part of this picture is adding dye to your finish coats - that tends to give you a deep semi transparent finish where the grain shows thru bu t does not specifically highlight the grain. You can do various things with the color including sunburst and finishes that become darker as you move to the edge (I define a sunburst as two or more colors that fade into each other where the guitar in your picture seems to be one color getting darker towards the edge).
This is a "clown burst" - amber in the center turning red on the outside. Most of them have larger amber areas but this customer wanted a "red guitar"
The fourth option is solid color - I don't do these but I have a friend who is one of the best motorcycle painters in the world and he does them for me - he uses automotive finishes and techniques.
As far as your question about pore filling - only certain woods have open pores that need filling - they tend to be the hardwoods like mahogany, rosewood, koa. Maple, spruce, cedar, alder, etc don't need it. Pore fillers can be pastes or other thickening materials or something like epoxy or CA. Basically you spread it on, then try to wipe or squeezie it off, leaving just a bit in the pores. Pore fillers often contain some stain - most of the time mahogany is filled with a redish brown paste filler. It can affect the look of the wood but usually not much.
Dan Erlewine's book is the bible on guitar finishing (StewMac) and I buy most of my finishing products from theme because I know they will work together. The real key to finishing is to experiment on cutoffs and scraps of the same wood that you are building from - I keep all my scraps for each guitar.