Either way works fine. Vertically, they prime a little better. Depending on the position of the manifold and such, there can be priming issues.
WIthout knowing your system, I cannot say for sure, but as a general rule, as long as they are below the water line, AND an air bubble cannot get trapped in an elbow or something, then you will be fine. The air bubble trapping can be frustrating if it happens, but usually a simple positioning difference fixes it.