OK, so it is clear that you will need to be able to get onto and off of the saddle with ease so that you can stand up in front of the saddle when stopped. I would find an area away from traffic and try Carbonfiberboy's suggestions about starting and stopping in the above post.

Your knees should not normally hit the handlebars, and I'm surprised that they do. If they do hit when the handlebars are in a good position, the bike is likely wrong for you. Are your handlebars rotated downward, or are they more like in the picture above that you supplied? For this kind of bike they are meant to look roughly like in the picture above so that your position is fairly upright.