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.
I've got a Thinline build set of parts coming in next week; had originally ordered clear grain filler to do the finish, but just ordered cans of StewMac brown and black filler as well... Might want to use the brown, depending on how you want to get the final result to look; I'm still waffling between going Gibson SG Special walnut or cherry on this build, will use the brown filler if walnut, black if cherry....
As far as I can tell - Warmoth uses a clear filler/sealer on mahogany. Gibson uses a very light filler on the LP goldtops, with darker filler on the other natural back models, and on the red or brown back models too.
C.F.Martin uses walnut colored filler (dark brown) on mahogany.
The dark filler only "enhances" the grain and pores. Clear filler like Warmoth uses (which may just be a sanded back later of finish, I dunno) leaves a bit of a sparkly grain, as the filler acts as microlenses in the light.
I think on Koa and Mahogany, I'd do a dark filler (carefully mask the top please!) on the body and sides, doing three fill coats for a full gloss finish (assuming StewMac water based filler). The top would be done in clear filler (now mask the sides). Again. multiple fill coats for a gloss finish.
To each his own I guess, depends on your vision of the finalized instrument.