You want to use pads in places where you will be soldering a component lead.  Feel free to connect traces to the pad on either layer.  Vias are used where you just want to pass a signal from one layer to the other.  Vias are not used to solder in components.

Physically pads and vias are identical.  They both are made using the same process.  Each have copper rings on the top and bottom layers and are connected together with a plated through hole.

They differ in how the ExpressPCB program handles them during your editing process.  When connecting traces, the ExpressPCB program may choose to eliminate a via if traces are connected to it only on one layer.  If this happens, you will see the via has been removed.