Ok. I always recommend people to start from 3d model. Here is a quick guide of how to setup Blender to render isometry and import your sketch into it.

First of all, Clint Bellanger has nice tutorial, about setting up isometric cameras:

http://clintbellanger.net/articles/isometric_tiles/

To summarize it:

1. start from empty scene, add camera.

2. set camera to orthographic projection

3. move camera to x,y,z = 10,-10,10

4. rotate camera by 60,0,45

5. add square plane (through add->mesh) for tile-size reference

Now you probably have your concept art done. It can already be the first pixelart frame, either isometric, or in front/left/top view. In any case, you want to import it into the scene for reference.

Blender has "add background image" feature, but I recommend simply importing your reference as a square, perpendicular to the camera. That way you can immediately compare your model with it.

To do that

1. Add plane, just like you added floor tile previously.

2. Load your sprite as texture, create material for it.

3. Press add UV map under squares's mesh properties. (it will set texture coordinates to match square to the image, so make sure you art is in square form)
4. If art is already isometric, then rotate square by 60.8553,-7.44692,31.9421

5. If reference art is a sprite on transparent background, then under texture pick color=1 and alpha=1, while under material enable transparency, set alpha=0, and specular=1. That will make sprite transparent, as it appears in game.

6. Now disable reference art square from rendering or move it to non-rendered layer.

Finally depending on your preference, you either create new model from that reference art, or import some existing public domain model, say from https://www.blendswap.com and use it as a puppet to help you with animation and dimensions.

For example, I used this dragon https://www.blendswap.com/blends/view/68233 to produce side angle for a dragon in my game. Of course it doesn't match perfectly, but has similar anatomy and gives you general idea, how it should be drawn.

Of course Blender is notoriously harder for newbies than 3ds Max or Maya, but it comes at the cheap price of nothing Still if you know easier and cheap alternatives, let us know!