Sadly there isn't really an easier way, you will need to put every sprite on it's own sheet for this system. At least that is what I found I had to do. It is a bit of work, but as it's a really good system, I believe it is worth the effort.
As far as VX tilesets in ACE, yes you can use them, but I think Ace comes with the VX tilesets included already. I may be a bit off here though,