It is possible. It might not be that good of an idea if it makes it hard to identify which line goes with which axis (using subplot & linkaxes is probably a better idea).
What you need to do, is get the line object for the curve you want to do something to, and tell it to set it's properties....
[axishandles curve1handle curve2handle] = plotyy(....);
get(curve1handle) % This will give you a list of properties you can change...
set(curve1handle,'property','new setting')
