Just set up a standard camera to use to render all the shots. If you use the same camera object you should be able to easily tell if your object is scaled correctly and how it is going to look in your 2D engine. Play around with different angles to see what works for you. Try a camera sitting at 100,100,100 and looking at the origin. In an isometric projection that gives you a 45 degree angle to all the axes. Really, all of your sprites will probably need tweaking anyway, no matter how you render them. What program are you using?

http://www.quanta-entertainment.com/isometricviewinmax.htm

Exactly!