Not sure about the Koa but you'll want to fill the pours of the mahogany for sure. As for colour its purely dependent on what you want, I would say that the colour of filler you use doesn't have that much impact on the final colour anyway, certainly less than I expected.
Most people tend to go for a darker filler like dark brown or a colour described as "Mahogany" which is a reddish brown.
How dark is your mahogany? I'm getting good results using "natural" coloured filler on a very pale mahogany body, its filling the grain with a very light -almost white- colour, looks really different to the usual dark fillers.
Saying that I imagine if your body has Koa top it will all be a dark guitar so I'd probably go for a darkish filler.
As for steps, well its not too complicated but it is hard work! Add the filler, wait about 5-10 mins until the colour dulls then scape as much of the excess of as you can. Seriously, if you leave to much on you'll be sanding for weeks it dries incredibly rock like.
Read the threads "finishing mahogany in tung oil" on here or "really basic question" where CB and Tonar give me all the wood filling advice you'll ever need (thanks again guys!). Should really help you out.