Can you post photos. It sounds like the key is getting water to drain off the topper. If water is pooling, you need to angle the cover somehow to correct that.
I agree some pics could go a long way. Some fabric covers are also better at repelling water than others. The basic "canvas" types would be on the lower end with multi-coated fabrics up at the top. I have stayed is some "fabric" covered yurts that were completely weather tight.
If you are using canvas, there is basically no way to keep it from pooling since you probably have it secured at the lowest end because of size. If you intend for this to be a weathproof structure, then you have to put on some sort of roof. Otherwise, it will have to serve as a fair weather spot only. If you decide to roof, you will need to use a rigid product or at least a semi-rigid product which will have to be caulked against leakage.
I had the same issue with mine, and we used the water repellent for tents. Scotch guard works pretty well too, but it takes several coats.
Thanks so much for the ideas, I will try to post pics this week.
Try the waterproofing spray for shoes. That works really well. Also make sure it is pulled tight enough so that it can't pool as much.