I'd second Dan and Brian: you'd want to look at stability and drag and I think a scale model is a good design tool for that - towed at steady speed along a dock or in a pool. It would give you a great feel for the stability and you could also use a gauge like Brian says to determine drag. What you choose to do depends on your interests, how much time you want to spend on this, and how fast of a sub you really want.
So please skeptically review the assumptions and opinions below as I'm rusty on this stuff - but if you go the model route you should first figure out how fast you can comfortably tow your model and work from there. Or better, how large of a model you care to build. I don't know your experience with this stuff but here's a link to an explanation on Reynold's numbers and the formula. Reynold's Nums are used, among other things, in model testing to get similar behavior of the fluid when the speeds, viscosities or sizes are varying from the full scale craft.
http://en.wikipedia.org/wiki/Reynolds_number#Example_on_the_importance_of_Reynolds_number
If you can test your model in the same water (temp and salinity) that you'll operate your sub in you can pretty much skip the formulas for casual testing. To find your model tow speed just multiply the full size speed by one over the scale. So a quarter-scale model requires a tow speed of four times the full size craft.
To look at submerged drag with your model you can hopefully again simplify a lot by using your 'operational' water for testing. The drag force measured on your model when towed at four times the full-size speed should equal the drag you'll see on the real sub.
http://en.wikipedia.org/wiki/Dynamic_similitude
Otherwise if you want to do it all on a PC I found Aerologic's Digital Wind Tunnel package (haven't tried it), but it goes for $3750:
http://www.aerologic.com/index.html It includes pre- and post-processing bits and lets you do stability calculations. You can get just the fluid dynamic calculation bits from NASA for I think $700:
http://www.openchannelfoundation.org/projects/PMARC_12/
Aren't the Rhino plugins just for surface boats? I only noticed calculations related to surface effects, planing drag and the like. ??
On a PC you could see, theoretically, what the flow would be around your sub. If you wanted to really get into the streamlining and performance for a faster vessel like DeepFlight this should help. Or again the physical model version of this is to mount your model in a "water tunnel" and inject dye into the water to see the flow lines. The general impression I have though is that scale model testing does give a better idea of the vehicle behavior - and the larger the scale the better - ideally 1:1! :-)
You could pull it through the water with a boat at
a given speed and then measure the force using a spring gage in between the pull
rope to determine how much force would be required to move it.