Whenever I'm doing bodywork I always use Isopon P40 and P38, fantastic stuff and easy to work with.
P40's used as a bridging filler...I tend to use this if I have a big gap to bridge or a lot of filling to do. Fill the majority of the hole up with this then apply the P38 to give the fine finish thats needed.
There's no real rule as to how many layers you need it's just a case of applying it and sanding it back until you get the desired finish. Generally it's best to use as little filler as possible in order to minimise it cracking as it drys out hence using the P40 for most of the filling.
Finally once your happy with the finish give it a light coat of primer, this not only helps to seal the filler but also shows up any imperfections...no matter how good you think the finish is once the primers on you'll notice there's still some imperfections, sand the primer back apply some more filler and repeat until it's right.
Hope this helps.
Ash