Hi Jade,
I think it should be straight forward especially if you custom app has its own data model after all you are writing to Aolserver rather than ACS. ACS is just the data model. So you may be binding some data model stuff like user_id and others. And your custom app may run straight from acs_root/www but you can then make it into acs_root/packages/custom_app/www.
I think the only way to find out is to try it.