Your first problem is just that, a problem. Controling a second file with the first is something they say can't be done. However, I am working on doing just that, and am almost finished. Once I am done I will let you know how I did it.
The second one is easy. Instead of having the sub btns show up on mouse over, put them in a nother frame, on another layer.
On your time line you will need a code like this:
Then on frame 2 make your sub buttons.
I added this effect to the swf and fla in the links above, refresh your browser and check them out again.