Any model built using a version of EwE5 later than version 1.67 can be converted to EwE6 format using the Ecopath database conversion wizard (see note below).
When you select the old database using Open model on the File menu? you will be prompted by the wizard to choose a model to extract from the old database. Select the model and follow the prompts. EwE6 will extract the model to a new database and save it in the Ecopath with Ecosim 6 folder (where you saved EwE6 on installation - usually in Program files).
EwE6 no longer supports multiple models in the same database.
Note: To check the version of your EwE5 model, open the model's database with MS Access and open the table called "Database specifications". The version of your model is the last (i.e., highest) number listed in the Version field.