Hello Paul
I had a look at the model (it is a fibreglass hull with twin propellers, isn't it?) and think you could use the same method that I found worked well:
First, you need to work out where exactly the holes for the propshafts go, drill them and file them out to an oval shape, large enough so the shafts do not have to be forced to their later position, yet as tight as possible.
Then you can make two jigs from plywood, that hold the shafts in place while gluing. I hope these sketches say more than a thousand words:
The jigs have holes the same diameter as the propshaft (the actual shaft, not the pipes around them (what do you call those in english?)), so they can be fitted on the shaft and clamped to the "pipe" by the ring inside and the nut outside. The jigs with the propshafts between them are attached to the hull with adhesive tape (an alternative approch would be glue them onto a length of adhesive tape that's been stuck on the hull). Now the shafts should be held in place.
At this time it would be a good idea to test fit the engine, coupling and propellers to make sure there is enough clearance.
Finally, I felled the hole from the outside with Blue Tack to prevent any spillage of glue to the outside. As glue i used polyester body filler, but any sort of two-component resin should do.
Hope than helps, it did work well on my boat.
Peter