http://iscoresports.com/

Recently had our first shootout and needed to place a player on 2nd base. I could not figure out how to put a player there. This was a case with 0 outs and no count. I have no idea how I would put a runner on base and add to the count and outs without messing up the hitters/pitchers stats. Is there a way to do this and I just can't find it?

I believe you are referring to a tiebreaker scenario.. If so

MISC> TIE BREAKER

Let's you choose runners to put on a base to start an inning. Do that to start an inning and then score as normal.