I'll add to v-joe's answer that you should never, ever modify the
Startup-Sequence. Since Release 2.0 the
Startup-Sequence was declared for private use by Commodore, because the system boots in a way to improve compatibility with releases 1.x.
In particular, the combination of
IPrefs enable advanced features that otherwise stay disabled (the most important one is
Intuition to use new fetch modes when running under an AGA machine, but there are other tidbits too). How the two commands interact was never fully documented, and probably not even tested by Commodore, so adding anything in-between is looking for undefined behavior.
It's occasionally required to run commands before
SetPatch, but these are commands that mess with the very low levels of the OS, such as developer's tools, debuggers, commands that play with the MMU, or tools to configure third-party accelerator boards; in this case the command's documentation will explicitly say to add it before
SetPatch, and you can trust them.
Bottom line: if you need to run DOS commands during the boot, use the
User-Startup mechanism introduced in Release 2.0: create a file named
User-Startup inside the
S: assign (if it is not already there; it usually is) and add your command(s) there. For the record, this is also where
Install adds commands required by third-party application.