According to the Propel API Docs you can define a database connection in your schema.xml file in such a manner:
<?xml version="1.0" encoding="UTF-8"?>
<database name="bookstore" defaultIdMethod="native">
<!-- table definitions go here -->
</database>
Then in your runtime-conf.xml settings you can set the connection params:
<datasources default="bookstore">
<datasource id="bookstore">
<adapter>mysql</adapter> <!-- sqlite, mysql, mssql, oracle, or pgsql -->
<connection>
<dsn>mysql:host=localhost;dbname=my_db_name</dsn>
<user>my_db_user</user>
<password>my_db_password</password>
</connection>
</datasource>
</datasources>
-- Edit --
Doesn't appear that Propel supports an alias attribute for the database tag, but you should be able to get away with the following:
<?xml version="1.0" encoding="UTF-8"?>
<database name="bookstore_primary" defaultIdMethod="native">
<!-- table definitions go here -->
</database>
<database name="bookstore_secondary" defaultIdMethod="native">
<!-- table definitions go here -->
</database>
<datasources default="bookstore_primary">
<datasource id="bookstore_primary">
<adapter>mysql</adapter> <!-- sqlite, mysql, mssql, oracle, or pgsql -->
<connection>
<dsn>mysql:host=localhost;dbname=bookstore_primary</dsn>
<user>my_db_user</user>
<password>my_db_password</password>
</connection>
</datasource>
</datasources>
<datasources default="bookstore_secondary">
<datasource id="bookstore_secondary">
<adapter>mysql</adapter> <!-- sqlite, mysql, mssql, oracle, or pgsql -->
<connection>
<dsn>mysql:host=localhost;dbname=bookstore_secondary</dsn>
<user>my_db_user</user>
<password>my_db_password</password>
</connection>
</datasource>
</datasources>
See if that works. At the end of the day the thing that really matters is that a connection can be made to both databases (using respective DSNs).