The reason for putting a reference to your program in the autoexec.bat was to load up the program into the memory of the computer on startup. This was to make the program resident in memory.
If you want or have to do that, you can just create a shortcut for your program that executes it whenever you double-click it and cut and paste it into the startup folder of the Programs Menu:
C:\Documents and Settings\[Your Profile]\Start Menu\Programs\Startup
(or you can use the Task Bar and Start Menu utility on the Settings menu, or drag and drop the shortcut into the Start\Programs\Startup menu)
That way everytime you start up Windows your program will load up into the memory of the computer -- that's what the startup folder is for -- you no longer need the autoexec.bat file.
I would install the program (or copy the program files) into a folder into a sub-folder of C:\Program Files folder. Something like this:
so that it is included within the path of the exectable files.
Your shortcut should have something like this:
Target: C:\Program Files\Memctrl\Memctrl.exe
Start in: C:\Program Files\Memctrl
One caveat though, your program may be dos based program -- WinXP emulates DOS, not a real one, so your program may or may not be compatible.
DOS programs for sure don't run on Win 2000, so don't try that. 95 and 98 were DOS compatible, but very inferior Operating Systems. WinXP may still be DOS compatible, I don't know. I haven't used any DOS programs for years.