Customers give the business money for the goods. It could be directly to the boss, or other employees of the business. When we say the customer pays the boss in this case, "pay" refers to an uneven relationship between the customer, the business, and the boss. The business has a product that the customer doesn't have or doesn't have the means to produce, so they give the business money to obtain it. In this relationship, it is considered appropriate for the company to charge more than it costs to produce the good. The price is set by the boss, who decides what profit is achievable, and what they are willing to do to maximize that.

In the poem the worker is said to pay the boss because the employee is in a similar position as the customer. In this case, they are giving the boss a higher value than they are receiving from the boss. They are exchanging their labour and the finished goods in exchange for two items the boss has a monopoly on: money (which is required to obtain goods in a system where you are alienated from the fruits of your labour), and access to the means of production.

You could simplify the "labour and the finished goods" for surplus labour value. I hear some guy wrote some compelling books about how many yards of linen a coat is worth. Might be worth a gander.