The .conf file is by default stored in the user profile directory, yes. If you don't need to edit the .conf file regularly, I think you can store it in the same directory as DOSBox.exe, and then delete the copy in the user account directory.
http://www.dosbox.com/wiki/Dosbox.conf#Creation_and_Location

I tried deleting the user .conf file but DosBox recreates it. I tried using a shortcut pointing to the main DosBox installation folder .conf file but it is ignored and recreated.

What command are you using in your shortcut?

I have no switches set to it currently. I was hoping it would have worked with that .conf shortcut pointing to the modified one.

I'm afraid you're not making any sense. What do you mean by ".conf shortcut" ? If you're not setting switches, what do you mean by "a shortcut pointing to the main DosBox installation folder .conf file" ?

I am trying to say that, I put a shortcut to my custom .conf file from my admin account, in the limited domain account's appdata folder, to test and see if it would run it but instead, it created a new one.

I will restate my question in this manner,

I am running program using DOSBox but need all domain accounts to run the same .conf file. Currently, every different account that runs DOSBox creates it's own .conf file in the \addpata directory. How can I make all domain accounts use the same .conf file in the local machine. I am running Windows 7 Ent.

set the shortcut to dosbox correctly so it uses the configuration file you want.

(so remove -userconf and add -conf path/to/your/config/file

eddieduce wrote:

I am trying to say that, I put a shortcut to my custom .conf file from my admin account, in the limited domain account's appdata folder, to test and see if it would run it but instead, it created a new one.

So you were expecting DOSBox to treat a shortcut to a .conf file like an actual .conf file? DOSBox does not work that way; very few applications do. Shortcuts are only useful in Windows Explorer.

As Mr. Qbix says, you will need to set the -conf switch in your DOSBox shortcut (i.e. the shortcut that launches DOSBox). You will also have to store the .conf file in a folder that the limited account can access.

[Thread moved to DOSBox General Section]

Qbix wrote:

set the shortcut to dosbox correctly so it uses the configuration file you want.

(so remove -userconf and add -conf path/to/your/config/file

I added the switches and it worked. Thanks a buttload.