Hi @AutumnSounds, you might not be able to use the wizard for that game. A batch file won't work for the application EXE, but what you can do is leave the application path blank, and then put the custom commands in the DOSBox configuration.
When you edit the game, in the DOSBox tab, you can create a custom configuration for the game. Then when you edit the configuration, under the DOS tab there is an Autoexec section; that's where you put in the commands. Keep in mind that the CD should already be mounted, assuming that you've added it to the mounts tab.
As for swapping discs, you can add both discs to the mounts tab under the same drive letter. Then there's a keyboard shortcut in DOSBox to swap discs; I don't remember what it is but a quick search should find it. :)
Let me know if you need more help and I can answer your questions.