You need to use the fbx-exporter from blender. The 3DGS-exporter from ventilator supports vertex animation only.
You can't export the animations from MED to blender, at least not in a way that I had figured out. Maybe, you just mixed it up in your question. If you meant how to export from blender to MED: it doesn't matter how you apply the weights, as far as I remember Acknex only supplies two weights.
If you don't have the Pro or Com version, you can't use bones weights in the engine, then you have to convert it to vertex animation to get the proper deformations.