many smaller filters use a sponge for mechanical filtration as well as the substrate for the bacteria to grow on. If your filter can only accomodate a sponge and a charcoal bag, yes, the charcoal will become a substrate for the bacteria as well as the sponge. Activated charcoal has its proponents, but many think it is of little value and is a poor bio-susbstrate. Thus, if you can substitute the charcoal with another form of biologic substrate like ceramic noodles or pourous rock, you might be better off. but many of the small filters only accomodate the cartridges that are solf for them, so this may not be possible.
If there is a spot that you can put a mesh bag that is downstream from the sponge, you can buy some biologic substrate (merely a material with a large surface area for bacteria), put it in the bag, and let it sit in the filter.