Hi,
It all depends on your code. You should be able to use Access as the database backend for your custom controls, but I don't really recommend it. If you decide to switch your custom controls to MSSQL, you will have to rewrite your sql code to work with MSSQL and you'll have to recreate your data structure.
We really can't guess about your custom controls, but just wrapping them in mojo isn't necessarily going to make them work with mojo.
HTH,
Joe D.