You may be confusing two terms here:
Solder mask is the laquer coating (most often green, but other colors are available) which covers most of the PCB, expect for the pads where you want to solder. Those must remain free of solder mask, so the solder can reach and wet the pads. Eagle shows the areas which are kept free of solder mask in the "tStop" and "bStop" layers. This applies to SMD as well as through-hole components, and the tStop and bStop layers show both, SMD and through-hole pads.
The "tCream" and "bCream" layers in Eagle show where solder paste will be added. This is only relevant for SMDs. These layers will not affect your PCB itself in any way. They will be used to manufacture a stencil (a separate piece of sheet metal or plastic to use as a mask for applying the paste), if you order one from the PCB manufacturer.