I think that you'd have the supercharger upstream of the turbo, as you say, ie. the supercharger fed directly from the airbox.
In the early days of supercharging or turbo-supercharging the term intercooler was coined to describe cooling devices that were present in-between each stage of sequential supercharging, hence 'inter'.
Based on this, and if there is room to do so (and subject to other concerns such as very long pipe runs) you could potentially go thus:
airbox(filter) - MAF - supercharger - intercooler#1 - turbocharger - intercooler#2 - inlet manifold.
Whether this is practical with a car engine I don't know. In rail traction and aircraft the engines generally run at steady revs for extended periods so lag and delayed response is not an issue. I imagine that with a car this could lead to lots of pumping losses and a very laggy pedal response due to the sheer length of the pipework.
Having said that, VW has a 1368cc petrol engine that uses supercharging and turbocharging which yields something like 170bhp!! I have no idea exactly how it's plumbed but clearly this is a very effective way of getting an engine to punch above its weight.
The engine even makes an appearance in the new Skoda Superb (although not yet in the UK), which is a heavy car. By all accounts it's disturbingly lively. I imagine that VW has had to build the four cylinder engine to the same industrial strength as would be found in a naturally aspirated 3.0 V6 to cope with the torque it's pushing out.
In terms of efficiency and packaging it has to be admired. I have yet to drive one so cannot comment personally.