This approach should work fine.
If you have several test environments on the same server, you can use multiple adTempus instances to support them all.
When you say "the naming convention will be different," are you referring paths to executables and other files, or to something else? The best way to handle that is to define Job Variables at the server level on each adTempus server for your paths, then use the variables in the jobs instead of hard-coding the paths. That way you don't have to change anything when you move the jobs from one environment to another.
So for example if your Development server has all the programs you are running under the "d:\devprograms" folder, you could define a Variable named "ProgramRoot" and set it to that path. Then in your jobs you would run "%ProgramRoot%\program1\program.exe", etc. On the other servers you would set that variable to the appropriate path for that environment.
The key is to set the Variables at the Server level so that they're not affected when you import the jobs from one environment to another.
We don't recommend that you try to modify data in the export file. If there are things that you need to have change between environments that you can't accomplish using Job Variables, let me know so we can help you find the best solution.
Right now the only way to do export/import is manually, through the Console. We have it on the to-do list to create a command-line tool so the process can be automated for deployment scenarios like yours. Let me know if that's something you're interested in pursuing.