Das kann man unter anderem auch über Parameter machen. Ich habe dafür mal was geschrieben.
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#RequireAdmin
[/autoit] [autoit][/autoit] [autoit]$PathSource = FileOpenDialog("Script auswählen", @ScriptDir, "Au3 Scripts (*.au3)")
$IconPath = FileOpenDialog("Icon auswählen", @ScriptDir, "Icons (*.ico)")
$Complevel = InputBox("Kompressionslevel", "0 - 4", 2)
$UPXPack = InputBox("UPX", "Mit UPX packen? 1 = Ja; 0 = Nein", 1)
If $UPXPack = 1 Then
$UPXPack = "/pack"
Else
$UPXPack = "/nopack"
EndIf
$ANSI_Unicode = InputBox("ANSI/Unicode", "1 = ANSI; 2 = Unicode", 2)
If $ANSI_Unicode = 1 Then
$ANSI_Unicode = "/ansi"
Else
$ANSI_Unicode = "/unicode"
EndIf
$Console = InputBox("Konsole/GUI", "1 = Konsole; 2 = GUI", 2)
If $Console = 1 Then
$Console = "/console"
Else
$Console = "/gui"
EndIf
$PathDest = FileSaveDialog("Speichern unter", @ScriptDir, "Exe (*.exe)")
RunWait(StringTrimRight(@AutoItExe, 11) & "Aut2Exe\Aut2exe.exe /in " & $PathSource & " /out " & $PathDest & ".exe /icon " & $IconPath & " /comp " & $Complevel & " " & $UPXPack & " " & $ANSI_Unicode & " /x86 " & $Console)
RunWait(StringTrimRight(@AutoItExe, 11) & "Aut2Exe\Aut2exe.exe /in " & $PathSource & " /out " & $PathDest & "_x64.exe /icon " & $IconPath & " /comp " & $Complevel & " " & $UPXPack & " " & $ANSI_Unicode & " /x64 " & $Console))
Es gibt aber auch andere Möglichkeiten.