I have a ltd company. Under the ltd company umbrella I have established a sole proprietor ship. I have to obtain a gst #. Do I register the Ltd ,with the GST#, or do I register the proprietor.

If you are providing services, you will have to charge goods and services tax on your invoice, so yes in order to obtain a GST # (this is Ontario folks) you will have to register under the name you are going to use when you invoice.