From what I have learnt through setting up am A3000 using WinUAE, is that you set which partition you want as default. Most people would use the default setting and have WB2 set as default.
If you hold both mouse buttons down on booting then you are presented with the dual boot screen where you can choose to boot from WB2 or WB1.3.
Also I believe holding down the esc key (may be another key) during boot brings up another menu where you can choose between 68000 & 68030 cpus, although, obviously, I can't get that to work in WinUAE.
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