plotyy is somewhat limited in that it can only take the two sets of x,y data so you have two choices --
a) make custom function that takes care of the desired customization but itself is callable by plotyy (I recall S Lord gave an example here not terribly long ago as in a few months at most that illustrated the idea nicely; sorry I can't recall the exact title), or
b) forego plotyy and draw the two axes individually. This really isn't as hard as it seems; and there's an example in the graphics help files section on enhancements that illustrates it.
Oh, and I guess there's a third...
c) take the basic bar that plotyy gives and then mung on the properties. With bar I suspect this is the least pleasant of the choices; for line plots it's generally straightforward and it may be w/ bar but I don't use it often enough to be particularly adept with it so I always struggle to get what I want that way...
ADDENDUM
Above is link to a thread where I posted S Lord's solution using anonymous functions for plotyy arguments. In the subject case it was fill instead of bar, but the idea's the same.