I had the same issue. Some of my products are supposed to cost less for the wholesale customers, so I used the lowest priced attribute in the main price or as the main price. Then you can subtract however much you want from that for the wholesale price. Next, you would set that attribute as an option that doesn't cost any extra if chosen.

EXAMPLE:

You are selling cards. The set is priced only by attributes.

10 cards = $10 (reg), $8 (wholesale)

20 cards = $15 (reg), $13 (wholesale)

But you want the cards to be cheaper for wholesale, so you set the base price of the cards as $10 for regular customers and $8 for wholesale customers. Then set up the attribute choices like so:

10 cards = +$0

20 cards = +$5 (that would make the total for 20 cards $15 for regular customers and $13 for wholesale customers).