I'm not sure I understand your question. Let me try to explain how the disk menu code works:
The menu items "Select Deathlord [TYPE] Disk..." allow you to specify the actual game disks that you will be using. These will be automatically swapped as necessary upon booting, rebooting, etc... The original game asked you if you wanted to use 2 drives for example, and that's now done by default and the game scenarios will be loaded automatically when you select "Play a game" in the menu.
And when you choose "Insert Boot Disk" or "Insert Scenario Disks" (or using alt-< and alt->), the game will automatically switch between the disks you've selected above.
The other menu choices are the "Insert Disk into Drive [1/2]". This acts as an override and specifically tells the emulator to load the given disk into a drive, but does not save any information. If you then choose "Insert Scenario Disks" for example, it will replace anything you had in the drives with the 2 scenarios.
To get back to your question, I think all you need to do is "Select Deathlord [TYPE] Disk..." on all 3 disks (boot, A and B), and choose the disks you want. Then play the game. You can see your current disks (and more) in the config file in Saved Games\Deathlord Relorded\DeathlordRelorded.conf