Is there anyway to setup CubeCart to where you can have a login for wholesale costs then everyone else logs in to have everything as regular prices? Or is the only way to pull this off is to just set-up two separate carts??

There are mods that do this - Check over at cubecartforums.org in the commercial mods section. Unfortunately not allowed to discuss mods here...

I just setup 2 stores to do this.

one for trade, one for retail and made the trade store registered users only which are authorised by myself.

I needed a special mod that Goober Cubemods created for me and now offers on his site.