I have an addon domain at hostmonster. They have a specific way of doing this, if domain.com is the main domain, then addondomain.domain.com = addondomain.com

If thats doesn't make sense then here...
I have www.habitatforbats.org
I also have www.bentfork.com
bentfork.com is an addon domain
so http://www.bentfork.com = http://bentfork.habitatforbats.org

Here is the problem, my store is for bentfork.com but when I upload it the URL gets re-written on all the generated store links.

i.e. http://bentfork.habitatforbats.org/eggstore/cart.php

I need it to be http://www.bentfork.com/eggstore/cart.php

I am referring to the site as www.bentfork.com
I am using the FTP account for bentfork.com
never anywhere to I define my h4bats domain.

Please advise.

/RB

I think you have done something wrong because when I click on both the links you mentioned above it does not go to your shop home page which should show as index.php instead of cart.php

Only a suggestion but in the top bar of the shopping where it says 'your shop', when you open it under where it says your website: what name did you type in there? Have you uploaded it with the shopping cart ftp programme? or uploaded it twice?

It might be a good idea to put in a support ticket.

Possibly others here might have another suggestions.