Well most commands end up in the C: assign which in most cases mean a drawer called c on the boot partition (SYS:). It's a similar case to the PATH variable in Linux. AmigaOS also looks for commands in places stored in PATH (just issue 'path' in shell to see what they are -- you can also add your own). If I remember correctly the order is as follows when the OS is looking for commands:
resident list (commands stored in kickstart or added via the 'resident' command)
current directory
drawers stored in PATH
EDIT:
I should have written $PATH since it's a variable
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