IP Networking

I have 2 different id's for an ftp destination. Each id handles files differently on the destinations end. Is it possible to have one destination machine and assign an alias name for each id. The .netrc file doesn't allow this.

Step-back-perspective question: Have you considered using ssh2/scp2 ?

Does it work with mixing the fully qualified domain host name, the unqualified host name or IP?

It always helps to know what Operating System and Shell you are running.
The following advice is general to mainstream unix Operating Systems and may well work with unix derivatives and variants:

The .netrc file is sourced relative to the value of $HOME.
The target ftp login name can be a parameter in a Shell "case" statement.
If you change and export $HOME just prior to invoking "ftp" you can have as many .netrc files as you like held in distinct directories. In your case this allows you to have multiple .netrc files for the same host all with different ftp login names.

Hope this helps.