I’m not as knowledgeable about technical grammar as some of the persons who comment on Italki, but I think the source of the confusion may be this: the sentence has only two independent clauses, and the third clause is a relative clause that really functions as an adjective. A relative clause is usually introduced by the word “that,” but here the “that” is omitted (see Chris’s comment below, inserting the missing “that”). One way to understand the sentence is: “It’s been hard work, but now (that the business is running smoothly) you can sit back and enjoy the fruits of your labors.” The relative clause that I have put in parentheses can be left out and the sentence is just two clauses joined with a “but” conjunction. Or, you can include the relative clause to provide, adjectivally, more information about what you mean by “now.”