Hi David and welcome to the forum

. Firstly, what sort of boat is it? It may well be that the centre is only just wide enough to fit the tube, and the way forward would be to drill a small hole and open this up with a file. A row of small holes could then be drilled along the likely length of cutout and similarly opened up. A Dremel or something similar is handy for this.

​Even if the slot goes astray a bit, you could use filler to hold the shaft in place, and then sand to suit the hull exterior.
​My personal method of fixing shafts is to chock them exactly in place and spot them with superglue to hold them as you want (and if you only use a couple of drips, the shaft could be released and try again)and then fill the gaps with filler or epoxy glue, or depending on your model, silicone sealant or similar.

​As well, you really need to have the motor either in position, or know exactly where the motor and its coupling will go before sticking the tube in. For a lot of models, the actual motor position does not matter too much, access is the usual driver, but on a sports boat then this matters a bit more. Similarly you need to allow room for the prop you intend to fit at the stern, and allow space for the prop to clear the rudder!

​A photo of the exterior and interior would help us assist more…see home page on how to make an album and so on.

​There is nothing to fear in fitting the shaft, as fitting the rudder tube and motor are equally as important. Workspace should not be an issue if you have space to carry on with the build afterwards. Drilling a few holes and a bit of filing will not take very long, and a thin marker line along the length of the hull will assist in "eying up" the shaft to get it straight with the hull.
Ashley