The AUTOEXEC.BAT file is used to list a set of commands that run when the machine first starts up. Some of these commands are used to configure the system like PATH, PROMPT, and SET TEMP. Other commands run memory resident programs that enhance your system. These can be things like MOUSE, SMARTDRV, etc.
The memory resident programs can have the unwanted side-effect of using up part of the main 640K memory that DOS uses for its programs. This can keep you from running certain programs. To avoid this, you can create a bootable system disk that doesn't have an AUTOEXEC.BAT. This will allow you to boot the system, without those initial programs running.
There may be some programs that are required by your system to allow it to function. This is especially true with compression programs. If this is the case, refer to your documentation for more information.
If you need to track down a conflict with a specific package, you can use a REM statement (see DOS manual). The REM disables the statement that follows it, turning it into a REMark. The procedure for doing this is to REM out all of your AUTOEXEC statements, reboot and see if the program works. If it does, edit your AUTOEXEC and start taking out the REMs, one at a time. Reboot between each change. If you remove a REM statement, and the program stops working. That line is your culprit.
For more information on the AUTOEXEC.BAT file, see your DOS manual.