ISBoxer - WoW Library Macros not working?

[MiRai]

The only thing I'm slightly confused on is what key combination to use for each macro, and whether or not it is necessary to set one (I get a warning if I don't)

It depends on how you have you have everything set up, but each macro requires its own unique key combination, and each macro set has its own unique macros.

It would help to see your profile.

[mbox_bob]

but each macro requires its own unique key combination, and each macro set has its own unique macros.

In an attempt to clarify that a little, each macro for a given Character needs it's own unique Key Combination. You can use the same Key Combination for different macros in different macro sets, provided that a combination of those macro sets using the same Key Combination will not be assigned to the same character.
This allows you to specify a macro in your Paladin Macro Set to use CTRL+SHIFT+Y and another macro for your Shaman Macro Set to use CTRL+SHIFT+Y, and they do completely different things.

Just be aware that when doing this, the class specific Macro Sets should be assigned to the Character, and not the Character Set, because when assigned to the Character Set, then all the characters in that set will get the macro, and you then may get error messages in game.