upgrade to the latest jdeveloper  version first !
u can run ur web based application  directly using the embedded oc4j in jdev.
if u mean an external deploy  and making a ear file then u need to make some profiles in jdev.
make a jar profile for ur model layers. then make the jar file.
make a war profile for ur web layer. then make the war file
make an ear profile for the whole application and then deploy to ear file .