I think I have multiple Byteball addresses in my wallet. Do I have to link them all with the bot to get blackbytes for each?
No, you don't get byteball based on byteball addresses. You get byteball based on Bitcoin addresses link to your byteball address(es).
To see what your byteball addresses are:
Click Home, then Cogwheel (preferences), Advanced, Wallet Information.... scroll to bottom.
Unless I misunderstood what you're asking.