You starting from a map or from scratch? With stand alone systems and no map, try and get some reference information, like from the manual as far as ignition timing goes, or to see other similar setups. Don't worry about creating the full map right away, just make it a big block to be on the safe side (full block rich..., or rather your fuel curve will look like a rectangle instead of some cool 3-D map.
Do you have access to a dyno and engine recording information? A dyno will be very handy with creating a baseline map. Also a means of measuring pipe temp and engine temp, well at least engine temp, is very important. It is difficult to tune with the engine constantly in varying operating conditions... changes in temp, pressure and the like.
The system probably has offset tables for engine temp and the like....
I haven't used the mega squirt, but I have used the Motec system quite a bit. From what I have seen, just getting an engine to idle is going to be your most difficult challenge. There are lots of things to check and verify and setup so the control system is actually doing what you think it is doing... lots of times problems arise from that.. Like the stupid motec changing what it's setting for the crank trigger is....
What is this project for? I would assume this is the 4 stroke phaser? You have any good books to read?
I would highly recommend this book. Very good info, and one of the guys from factory pro racing helped write it. I have talked to him a few times and he knows his sh!t... or at least much much more than I do / did.
I am not sure about snowmobiles, but most motorcycles are alpha -n based, which means the maps are changed by throttle position and rpm only.....(not accounting for changes in operating or environmental aspects..) there are not any means of actually measuring the amount of air coming into the engine. Alpha -n is mostly used because the changes in rpm are so vast and quick that any amount of time trying to measure something and then calculate is futile since the rpm has already changed. This is different then a car or automobile as changes are much much smaller and slower, and since they are operated at steady state conditions for a higher percentage of time.
Seriously check out the book, it will help give you some insight into what all the changes have an effect on. I am ticked I gave mine away.... but I guess that is a reason to buy another one.