One option is to configure the two instances with their own IP addresses and then you can use port 1433 on both.

This way you can use DNS for all your connection strings, odbc and so on and then you don't have to mess with aliases.

Using server\instance or random portnumbers in connectionstrings is administrative/migration hell..

So I've set a standard for the DNS entries:

SQL-ApplicationName.company.local

SQL-Databasename.company.local

And I use this for ALL SQL connections , this way it is easier to migrate/move in the future (just change IP for the host entry).

Also everything is documented in the DNS.

There are some things to think about when setting this up, reply to this if you are interested.