Sookie wasn't paid directly - Bill was paid (kind of like a manager) & then gave Sookie her "cut' so to speak. Eric didn't accept his flaky excuse, it's just at this point in the story, after Eric's line of questioning..he concludes what he already knew instinctively, that Bill is young, immature & trying to keep Sookie under his thumb & away from Eric. What better way to do that by controlling her money? So when Eric leaves,  he already knows it's over & that's the point...he knows Bill is an F-up & is saying (without directly saying) that he is on to him, has lost & Eric has just put himself in the running w/this huge bit of crucual information.

We find out, or it's implied in the actual series that Sookie didn't see much of her money from her job in LDID. It was a play on that aspect, twisted & given a perspective from Eric. Eric seeing what a shit state her driveway is in & wondering why his payment couldn't not only pay for a new drive but also her mortgage - makes the lightbulb go off in his head. 

So he is calling Bill out on what he did with the money she was paid (Eric knowing it was more than she was actually given). That convo was Eric's way of figuring out what happened from what he already deduced & then antagonizing Bill for being such an idiot & ending with him being smug (his being affectionate w/sleeping Sookie & then ordering Bill around in the next breath).

So the overall scene is showcasing one more large bit of information about Bill which confirms Eric's instinct about him. Eric doesn't need to be overt, he knows what he knows & he knows Bill knows it as well & he doesn't have to even come out & say it. His line of questioning & actions speak for themselves - that Bill is a fool & has lost the plot & Eric..methodical Eric is going to come out the winner.

Hope that helps.