Are the models new creations or ships already ingame?
If new creations, then open PCS2 go to options->preferences->lower left corner->cob scaling factor and use a value that fits your needs ( if the model in your 3D app is 15meters and you want exactly the size use a value of 1.00.
If the models are ingame already, extract the .pof files, open them in PCS2 go to save, then select as .cob from the drop down menu, save it.
Edit the value in cob scaling factor, load the previously saved .cob and check the size of the model.
You see it in the bottom right corner, it's model info, H: W: D: