Not sure exactly how you are doing this but I'll outline how I would approach this.
Set a wholesale flag in the user table.
Add a wholesale price or % off in the product table.
Every place a price is read, use something like this:
If wholesale get wholesale price
get regular price
You can search for all of the price variables by using this feature:
Find all instances of a variable in a site
In the admin pages, just add the wholesale price field so you can manage both from the same pages.