If you think that the number of zones will not suit your needs, then you can try moving the manifold or and then generating the design once again. The placement of the lines and sprinkler heads is normally dictated by the placement of the manifold. You can also try increasing the flow rate, as this can decrease the number of zones the designer thinks you need.
You can also try placing non-watered features where you do not want a zone if you do not wish to have that area watered at all.