To understand how commissions works, the easy way is to start with an example that shows how price classes works:

1) go to "Accounts" and create a new record in "Affiliate" tab.
2) in the "Preferences" pane make sure to set "Net price class" = "Travel agencies" and "Gross price class" = "Retail"
3) select a Hotel from the "catalogue" mask
4) make sure a valid price list is loaded by clicking on "Edit pricelist" link and checking seasons, rooms and rates.
4) click on "Set commissions" in the side menu (right)
5) add a new contract (click [+]) and make sure to set "Class to activate"="Travel agencies", then "Source"="Retail", then "Operation"="Commission" and finally "Commission/markup amount"="20" (or whatever percentage you like)

Now, to actually see how this affect the pricing for a Travel Agent (like the one account you created at step 1):

A) go to the public portal
B) click on "Login" and use the credentials (username and password) you assigned to your test account on step 1
C) go to the hotel you modified at step 3 and proceed to reservation.
D) you will see that a commission of "20%" is displayed beside the total of the accommodation in the reservation summary.

Probably in step 2 you wondered what are Net/Gross/RackRate price classes, here you go:

GROSS PRICE: is the price class used to display the price once the affiliate is logged in
NET PRICE: is the price class used to calculate the special condition granted to the affiliate. This is the class that should contain the commission.
RACK RATE: a rack-rate price can be displayed beside the gross price when we want to highlights good deals or display a street-price comparison (requires template customizations to add something like a stroke-through price)