Not immediately easy to answer, as it may run either way, as long as both admission ports aren't uncovered at the same time, but you will need a different setting of the eccentric.
Probably the top one, but without knowing dimensions of ports and valve cavity I can't be sure. It will effect events even if the cavity is square, as in the top arrangement you will get much earlier cutoff and more expansive working.
It may be that it runs better on air with the second arrangement, and on steam with the first 
If the cavity is rectangular, the answer is easy as I think Stuart usually make the valve cavity the same width as the ports.
Can you show a picture showing both the port face and the valve cavity? Or give some measurements?
Neil