This is actually a pretty straigtforward task you are trying to do. You need to create your own SOPC Builder component that interfaces to the EMIF on one side and has an Avalon Memory-Mapped master on the other. The glue logic between the two should be minimal.
1 - Let's assume you know and understand the EMIF specification well.
2 - Study the Avalon Memory-Mapped bus interface
http://www.altera.com/literature/manual/mnl_avalon_spec.pdf 3 - Write HDL code for your module. Obviously this will include:
a - Avalon Master port signals
b - EMIF port signals
c - Bus translation logic. You might wire straight across but more likely your are going to register signals between the two interfaces.
4 - Either :
Create an SOPC builder component. Use the Component Editor to import your HDL file. Assign your Avalon Master signals accordingly and create a "conduit" interface to export your EMIF signals. This will make your EMIF signals show up in the port list of your SOPC system.
or ...
Your other option is to do as you stated. Create a component using the Avalon Master template without any HDL code. This will export all of the Avalon Master signals outside of SOPC builder. Then you can write all of your HDL code outside of SOPC builder.
Jake